Coordinate Section

The Coordinate Section contains the collection of atomic coordinates as well as the MODEL and ENDMDL records.  


MODEL

Overview

The MODEL record specifies the model serial number when multiple models of the same structure are presented in a single coordinate entry, as is often the case with structures determined by NMR.

Record Format

COLUMNS        DATA  TYPE    FIELD          DEFINITION
---------------------------------------------------------------------------------------
 1 -  6        Record name   "MODEL "
11 - 14        Integer       serial         Model serial number.

Details

Verification/Validation/Value Authority Control

Entries with multiple models in the NUMMDL record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models.

Relationships to Other Record Types

Each MODEL must have a corresponding ENDMDL record.

Examples

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL        1
ATOM      1  N   ALA A   1      11.104   6.134  -6.504  1.00  0.00           N
ATOM      2  CA  ALA A   1      11.639   6.071  -5.147  1.00  0.00           C
...                                                                                                                                                  …
...                                                                                                                                                  …
...                                                                                                                                                  …
ATOM    293 1HG  GLU A   18    -14.861  -4.847   0.361  1.00  0.00           H
ATOM    294 2HG  GLU A   18    -13.518  -3.769   0.084  1.00  0.00           H
TER     295      GLU A   18                                           
ENDMDL                                                              
MODEL        2                                                       
ATOM    296  N   ALA  A   1     10.883   6.779  -6.464  1.00  0.00           N
ATOM    297  CA  ALA  A   1     11.451   6.531  -5.142  1.00  0.00           C
...                                                                                                                                                  …
...                                                                                                                                                  …
ATOM    588 1HG  GLU A   18    -13.363  -4.163  -2.372  1.00  0.00           H
ATOM    589 2HG  GLU A   18    -12.634  -3.023  -3.475  1.00  0.00           H
TER     590      GLU A   18                                          
                                                                                                                                                  ENDMDL
         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL        1
ATOM      1  N  AALA A   1      72.883  57.697  56.410  0.50 83.80           N  
ATOM      2  CA AALA A   1      73.796  56.531  56.644  0.50 84.78           C  
ATOM      3  C  AALA A   1      74.549  56.551  57.997  0.50 85.05           C  
ATOM      4  O  AALA A   1      73.951  56.413  59.075  0.50 84.77           O  
...
...
...
HETATM37900  O  AHOH   490     -24.915 147.513  36.413  0.50 41.86           O  
HETATM37901  O  AHOH   491     -28.699 130.471  22.248  0.50 36.06           O  
HETATM37902  O  AHOH   492     -33.309 184.488  26.176  0.50 15.00           O  
ENDMDL                                                                          
MODEL        2                                                                  
ATOM      1  N  BALA A   1      72.883  57.697  56.410  0.50 83.80           N  
ATOM      2  CA BALA A   1      73.796  56.531  56.644  0.50 84.78           C  
ATOM      3  C  BALA A   1      74.549  56.551  57.997  0.50 85.05           C  
ATOM      4  O  BALA A   1      73.951  56.413  59.075  0.50 84.77           O  
ATOM      5  CB BALA A   1      74.804  56.369  55.453  0.50 84.29           C  
ATOM      6  N  BASP A   2      75.872  56.703  57.905  0.50 85.59           N  
ATOM      7  CA BASP A   2      76.801  56.651  59.048  0.50 85.67           C  
ATOM      8  C  BASP A   2      76.283  57.361  60.309  0.50 84.80           C  
...


ATOM

Overview

The ATOM records present the atomic coordinates for standard amino acids and nucleotides. They also present the occupancy and temperature factor for each atom. Non-polymer chemical coordinates use the HETATM record type. The element symbol is always present on each ATOM record; charge is optional.

Changes in ATOM/HETATM records result from the standardization atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary (https://ftp.wwpdb.org/pub/pdb/data/monomers).

Record Format

COLUMNS        DATA  TYPE    FIELD        DEFINITION
-------------------------------------------------------------------------------------
 1 -  6        Record name   "ATOM  "
 7 - 11        Integer       serial       Atom  serial number.
13 - 16        Atom          name         Atom name.
17             Character     altLoc       Alternate location indicator.
18 - 20        Residue name  resName      Residue name.
22             Character     chainID      Chain identifier.
23 - 26        Integer       resSeq       Residue sequence number.
27             AChar         iCode        Code for insertion of residues.
31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
55 - 60        Real(6.2)     occupancy    Occupancy.
61 - 66        Real(6.2)     tempFactor   Temperature  factor.
77 - 78        LString(2)    element      Element symbol, right-justified.
79 - 80        LString(2)    charge       Charge  on the atom.

Details

Verification/Validation/Value Authority Control

The ATOM/HETATM records are checked for PDB file format, sequence information, and packing.

Relationships to Other Record Types

The ATOM records are compared to the corresponding sequence database. Sequence discrepancies appear in the SEQADV record. Missing atoms are annotated in the remarks. HETATM records are formatted in the same way as ATOM records. The sequence implied by ATOM records must be identical to that given in SEQRES, with the exception that residues that have no coordinates, e.g., due to disorder, must appear in SEQRES.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM     32  N  AARG A  -3      11.281  86.699  94.383  0.50 35.88           N  
ATOM     33  N  BARG A  -3      11.296  86.721  94.521  0.50 35.60           N
ATOM     34  CA AARG A  -3      12.353  85.696  94.456  0.50 36.67           C
ATOM     35  CA BARG A  -3      12.333  85.862  95.041  0.50 36.42           C
ATOM     36  C  AARG A  -3      13.559  86.257  95.222  0.50 37.37           C
ATOM     37  C  BARG A  -3      12.759  86.530  96.365  0.50 36.39           C
ATOM     38  O  AARG A  -3      13.753  87.471  95.270  0.50 37.74           O
ATOM     39  O  BARG A  -3      12.924  87.757  96.420  0.50 37.26           O
ATOM     40  CB AARG A  -3      12.774  85.306  93.039  0.50 37.25           C
ATOM     41  CB BARG A  -3      13.428  85.746  93.980  0.50 36.60           C
ATOM     42  CG AARG A  -3      11.754  84.432  92.321  0.50 38.44           C
ATOM     43  CG BARG A  -3      12.866  85.172  92.651  0.50 37.31           C
ATOM     44  CD AARG A  -3      11.698  84.678  90.815  0.50 38.51           C
ATOM     45  CD BARG A  -3      13.374  85.886  91.406  0.50 37.66           C
ATOM     46  NE AARG A  -3      12.984  84.447  90.163  0.50 39.94           N
ATOM     47  NE BARG A  -3      12.644  85.487  90.195  0.50 38.24           N
ATOM     48  CZ AARG A  -3      13.202  84.534  88.850  0.50 40.03           C
ATOM     49  CZ BARG A  -3      13.114  85.582  88.947  0.50 39.55           C
ATOM     50  NH1AARG A  -3      12.218  84.840  88.007  0.50 40.76           N
ATOM     51  NH1BARG A  -3      14.338  86.056  88.706  0.50 40.23           N
ATOM     52  NH2AARG A  -3      14.421  84.308  88.373  0.50 40.45           N
         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM     32  N  AARG A  -3      11.281  86.699  94.383  0.50 35.88           N  
ATOM     33  CA AARG A  -3      12.353  85.696  94.456  0.50 36.67           C
ATOM     34  C  AARG A  -3      13.559  86.257  95.222  0.50 37.37           C
ATOM     35  O  AARG A  -3      13.753  87.471  95.270  0.50 37.74           O
ATOM     36  CB AARG A  -3      12.774  85.306  93.039  0.50 37.25           C
ATOM     37  CG AARG A  -3      11.754  84.432  92.321  0.50 38.44           C
ATOM     38  CD AARG A  -3      11.698  84.678  90.815  0.50 38.51           C
ATOM     39  NE AARG A  -3      12.984  84.447  90.163  0.50 39.94           N
ATOM     40  CZ AARG A  -3      13.202  84.534  88.850  0.50 40.03           C
ATOM     41  NH1AARG A  -3      12.218  84.840  88.007  0.50 40.76           N
ATOM     42  NH2AARG A  -3      14.421  84.308  88.373  0.50 40.45           N
ATOM     43  N  BARG A  -3      11.296  86.721  94.521  0.50 35.60           N
ATOM     44  CA BARG A  -3      12.333  85.862  95.041  0.50 36.42           C
ATOM     45  C  BARG A  -3      12.759  86.530  96.365  0.50 36.39           C
ATOM     46  O  BARG A  -3      12.924  87.757  96.420  0.50 37.26           O
ATOM     47  CB BARG A  -3      13.428  85.746  93.980  0.50 36.60           C
ATOM     48  CG BARG A  -3      12.866  85.172  92.651  0.50 37.31           C
ATOM     49  CD BARG A  -3      13.374  85.886  91.406  0.50 37.66           C
ATOM     50  NE BARG A  -3      12.644  85.487  90.195  0.50 38.24           N
ATOM     51  CZ BARG A  -3      13.114  85.582  88.947  0.50 39.55           C
ATOM     52  NH1BARG A  -3      14.338  86.056  88.706  0.50 40.23           N


ANISOU

Overview

The ANISOU records present the anisotropic temperature factors.

Record Format

COLUMNS       DATA  TYPE    FIELD          DEFINITION
-----------------------------------------------------------------
 1 - 6        Record name   "ANISOU"
 7 - 11       Integer       serial         Atom serial number.
13 - 16       Atom          name           Atom name.
17            Character     altLoc         Alternate location indicator
18 - 20       Residue name  resName        Residue name.
22            Character     chainID        Chain identifier.
23 - 26       Integer       resSeq         Residue sequence number.
27            AChar         iCode          Insertion code.
29 - 35       Integer       u[0][0]        U(1,1)
36 - 42       Integer       u[1][1]        U(2,2)
43 - 49       Integer       u[2][2]        U(3,3)
50 - 56       Integer       u[0][1]        U(1,2)
57 - 63       Integer       u[0][2]        U(1,3)
64 - 70       Integer       u[1][2]        U(2,3)
77 - 78       LString(2)    element        Element symbol, right-justified.
79 - 80       LString(2)    charge         Charge on the atom.

Details

Verification/Validation/Value Authority Control

The depositor provides ANISOU records, and the wwPDB verifies their format.

Relationships to Other Record Types

The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic temperature factors as ,B(eq), as described in the ATOM and HETATM sections.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM    107  N   GLY A  13      12.681  37.302 -25.211 1.000 15.56           N
ANISOU  107  N   GLY A  13     2406   1892   1614    198    519   -328       N
ATOM    108  CA  GLY A  13      11.982  37.996 -26.241 1.000 16.92           C
ANISOU  108  CA  GLY A  13     2748   2004   1679    -21    155   -419       C
ATOM    109  C   GLY A  13      11.678  39.447 -26.008 1.000 15.73           C
ANISOU  109  C   GLY A  13     2555   1955   1468     87    357   -109       C
ATOM    110  O   GLY A  13      11.444  40.201 -26.971 1.000 20.93           O
ANISOU  110  O   GLY A  13     3837   2505   1611    164   -121    189       O
ATOM    111  N   ASN A  14      11.608  39.863 -24.755 1.000 13.68           N
ANISOU  111  N   ASN A  14     2059   1674   1462     27    244    -96       N

Relationships to Other Record Types

The standard deviations for the anisotropic temperature factors are related to the corresponding ATOM/ HETATM ANISOU temperature factors.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM    107  N   GLY A  13      12.681  37.302 -25.211 1.000 15.56           N
ANISOU  107  N   GLY A  13     2406   1892   1614    198    519   -328       N
SIGUIJ  107  N   GLY A  13       10     10     10     10     10     10       N
ATOM    108  CA  GLY A  13      11.982  37.996 -26.241 1.000  16.92          C
ANISOU  108  CA  GLY A  13     2748   2004   1679    -21    155   -419       C
SIGUIJ  108  CA  GLY A  13       10     10     10     10     10     10       C
ATOM    109  C   GLY A  13      11.678  39.447 -26.008 1.000  15.73          C
ANISOU  109  C   GLY A  13     2555   1955   1468     87    357   -109       C
SIGUIJ  109  C   GLY A  13       10     10     10     10     10     10       C
ATOM    110  O   GLY A  13      11.444  40.201 -26.971 1.000  20.93          O
ANISOU  110  O   GLY A  13     3837   2505   1611    164   -121    189       O
SIGUIJ  110  O   GLY A  13       10     10     10     10     10     10       O
ATOM    111  N   ASN A  14      11.608  39.863 -24.755 1.000  13.68          N
ANISOU  111  N   ASN A  14     2059   1674   1462     27    244    -96       N
SIGUIJ  111  N   ASN A  14       10     10     10     10     10     10       N


TER

Overview

The TER record indicates the end of a list of ATOM/HETATM records for a chain.

Record Format

COLUMNS        DATA  TYPE    FIELD           DEFINITION
-------------------------------------------------------------------------
 1 -  6        Record name   "TER   "
 7 - 11        Integer       serial          Serial number.
18 - 20        Residue name  resName         Residue name.
22             Character     chainID         Chain identifier.
23 - 26        Integer       resSeq          Residue sequence number.
27             AChar         iCode           Insertion code.

Details

Verification/Validation/Value Authority Control

TER must appear at the terminal carboxyl end or 3' end of a chain. For proteins, there is usually a terminal oxygen, labeled OXT. The validation program checks for the occurrence of TER and OXT records.

Relationships to Other Record Types

The residue name appearing on the TER record must be the same as the residue name of the immediately preceding ATOM or non-water HETATM record.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM    601  N   LEU A  75     -17.070 -16.002   2.409  1.00 55.63           N  
ATOM    602  CA  LEU A  75     -16.343 -16.746   3.444  1.00 55.50           C  
ATOM    603  C   LEU A  75     -16.499 -18.263   3.300  1.00 55.55           C  
ATOM    604  O   LEU A  75     -16.645 -18.789   2.195  1.00 55.50           O  
ATOM    605  CB  LEU A  75     -16.776 -16.283   4.844  1.00 55.51           C  
TER     606      LEU A  75   
...                                                                                                                                                  … 
ATOM   1185  O   LEU B  75      26.292  -4.310  16.940  1.00 55.45           O  
ATOM   1186  CB  LEU B  75      23.881  -1.551  16.797  1.00 55.32           C  
TER    1187      LEU B  75                                                      
HETATM 1188  H2  SRT A1076     -17.263  11.260  28.634  1.00 59.62           H  
HETATM 1189  HA  SRT A1076     -19.347  11.519  28.341  1.00 59.42           H  
HETATM 1190  H3  SRT A1076     -17.157  14.303  28.677  1.00 58.00           H  
HETATM 1191  HB  SRT A1076     -15.110  13.610  28.816  1.00 57.77           H  
HETATM 1192  O1  SRT A1076     -17.028  11.281  31.131  1.00 62.63           O  

ATOM    295  HB2 ALA A  18       4.601  -9.393   7.275  1.00  0.00           H  
ATOM    296  HB3 ALA A  18       3.340  -9.147   6.043  1.00  0.00           H  
TER     297      ALA A  18                                                      
ENDMDL                                                                          


HETATM

Overview

Non-polymer or other “non-standard” chemical coordinates, such as water molecules or atoms presented in HET groups use the HETATM record type. They also present the occupancy and temperature factor for each atom. The ATOM records present the atomic coordinates for standard residues. The element symbol is always present on each HETATM record; charge is optional.

Changes in ATOM/HETATM records will require standardization in atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary, https://ftp.wwpdb.org/pub/pdb/data/monomers.

Record Format

COLUMNS       DATA  TYPE     FIELD         DEFINITION
-----------------------------------------------------------------------
 1 - 6        Record name    "HETATM"
 7 - 11       Integer        serial        Atom serial number.
13 - 16       Atom           name          Atom name.
17            Character      altLoc        Alternate location indicator.
18 - 20       Residue name   resName       Residue name.
22            Character      chainID       Chain identifier.
23 - 26       Integer        resSeq        Residue sequence number.
27            AChar          iCode         Code for insertion of residues.
31 - 38       Real(8.3)      x             Orthogonal coordinates for X.
39 - 46       Real(8.3)      y             Orthogonal coordinates for Y.
47 - 54       Real(8.3)      z             Orthogonal coordinates for Z.
55 - 60       Real(6.2)      occupancy     Occupancy.
61 - 66       Real(6.2)      tempFactor    Temperature factor.
77 - 78       LString(2)     element       Element symbol; right-justified.
79 - 80       LString(2)     charge        Charge on the atom.

Details

Verification/Validation/Value Authority Control

Processing programs check ATOM/HETATM records for PDB file format, sequence information, and packing.

Relationships to Other Record Types

HETATM records must have corresponding HET, HETNAM, FORMUL and CONECT records, except for waters.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETATM 8237 MG    MG A1001      13.872  -2.555 -29.045  1.00 27.36          MG 
 
HETATM 3835 FE   HEM A   1      17.140   3.115  15.066  1.00 14.14          FE
HETATM 8238  S   SO4 A2001      10.885 -15.746 -14.404  1.00 47.84           S  
HETATM 8239  O1  SO4 A2001      11.191 -14.833 -15.531  1.00 50.12           O  
HETATM 8240  O2  SO4 A2001       9.576 -16.338 -14.706  1.00 48.55           O  
HETATM 8241  O3  SO4 A2001      11.995 -16.703 -14.431  1.00 49.88           O  
HETATM 8242  O4  SO4 A2001      10.932 -15.073 -13.100  1.00 49.91           O  


ENDMDL

Overview

The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.

Record Format

COLUMNS       DATA  TYPE     FIELD        DEFINITION
------------------------------------------------------------------
1 - 6         Record name   "ENDMDL"

Details

Verification/Validation/Value Authority Control

Entries with multiple structures in the NUMMDL record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models.

Relationships to Other Record Types

There must be a corresponding MODEL record.

In the case of an NMR entry, the NUMMDL record states the number of model structures that are present in the individual entry.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
...                                                                                                                                                  ...
...                                                                                                                                                  ...
ATOM  14550 1HG  GLU   122     -14.364  14.787 -14.258  1.00  0.00           H
ATOM  14551 2HG  GLU   122     -13.794  13.738 -12.961  1.00  0.00           H
TER   14552      GLU   122                                             
ENDMDL                                                                 
MODEL        9                                                         
ATOM  14553  N   SER     1     -28.280   1.567  12.004  1.00  0.00           N
ATOM  14554  CA  SER     1     -27.749   0.392  11.256  1.00  0.00           C
...                                                                                                                                                  ...
...                                                                                                                                                  ...
ATOM  16369 1HG  GLU   122      -3.757  18.546  -8.439  1.00  0.00           H
ATOM  16370 2HG  GLU   122      -3.066  17.166  -7.584  1.00  0.00           H
TER   16371      GLU   122                                             
ENDMDL                                                                 


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