Atomic Coordinate Entry Format Version 3.2
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
- This record is used only when more than one model appears in an entry. Generally, it is employed mainly for NMR structures. The chemical connectivity should be the same for each model. ATOM, HETATM, ANISOU, and TER records for each model structure and are interspersed as needed between MODEL and ENDMDL records.
- The numbering of models is sequential, beginning with 1.
- All models in a deposition should be superimposed in an appropriate author determined manner and only one superposition method should be used. Structures from different experiments, or different domains of a structure should not be superimposed and deposited as models of a deposition.
- All models in an NMR ensemble should be homogeneous – each model should have the exact same atoms (hydrogen and heavy atoms), sequence and chemistry.
- Deposition of minimized average structure must be accompanied with ensemble and must be homogeneous with ensemble.
- A model cannot have more than 99,999 atoms. Where the entry does not contain an ensemble of models, then the entry cannot have more than 99,999 atoms. Entries that go beyond this atom limit must be split into multiple entries, each containing no more than the limits specified above.
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://files.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
- ATOM records for proteins are listed from amino to carboxyl terminus.
- Nucleic acid residues are listed from the 5' to the 3' terminus.
- No ordering is specified for polysaccharides.
- Non-blank alphanumerical character is used for chain identifier.
- The list of ATOM records in a chain is terminated by a TER record.
- If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records.
- AltLoc is the place holder to indicate alternate conformation. The alternate conformation can be in the entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. Within a residue, all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator. There are two ways of representing alternate conformation- either at atom level or at residue level (see examples).
- For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:
- In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry. - In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together.
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
- Columns 7 - 27 and 73 - 80 are identical to the corresponding ATOM/HETATM record.
- The anisotropic temperature factors (columns 29 - 70) are scaled by a factor of 10**4 (Angstroms**2) and are presented as integers.
- The anisotropic temperature factors are stored in the same coordinate frame as the atomic coordinate records.
- ANISOU values are listed only if they have been provided by the depositor.
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
- Every chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record.
- The TER records occur in the coordinate section of the entry, and indicate the last residue presented for each polypeptide and/or nucleic acid chain for which there are determined coordinates. For proteins, the residue defined on the TER record is the carboxy-terminal residue; for nucleic acids it is the 3'-terminal residue.
- For a cyclic molecule, the choice of termini is arbitrary.
- Terminal oxygen atoms are presented as OXT for proteins, and as O5’ or OP3 for nucleic acids. These atoms are present only if the last residue in the polymer is truly the last residue in the SEQRES.
- The TER record has the same residue name, chain identifier, sequence number and insertion code as the terminal residue. The serial number of the TER record is one number greater than the serial number of the ATOM/HETATM preceding the TER.
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://files.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
- The x, y, z coordinates are in Angstrom units.
- No ordering is specified for polysaccharides.
- See the HET section of this document regarding naming of heterogens. See the Chemical Component Dictionary for residue names, formulas, and topology of the HET groups that have appeared so far in the PDB (see https://files.wwpdb.org/pub/pdb/data/monomers ).
- If the depositor provides the data, then the isotropic B value is given for the temperature factor.
- If there are neither isotropic B values provided by the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.
- Insertion codes and element naming are fully described in the ATOM section of this document.
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
- MODEL/ENDMDL records are used only when more than one structure is presented in the entry, as is often the case with NMR entries.
- All the models in a multi-model entry must represent the same structure.
- Every MODEL record has an associated ENDMDL record.
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