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Coordinate SectionThe Coordinate Section contains the collection of atomic coordinates as well as the MODEL and ENDMDL records. MODELOverviewThe MODEL record specifies the model serial number when multiple structures 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
Entries with multiple structures in the EXPDTA record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models. Relationships to Other Record TypesEach MODEL must have a corresponding ENDMDL record. In the case of an NMR entry the EXPDTA record states the number of model structures that are present in the individual entry. Example
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 MODEL 1 ATOM 1 N ALA 1 11.104 6.134 -6.504 1.00 0.00 N ATOM 2 CA ALA 1 11.639 6.071 -5.147 1.00 0.00 C ... ... ATOM 293 1HG GLU 18 -14.861 -4.847 0.361 1.00 0.00 H ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H TER 295 GLU 18 ENDMDL MODEL 2 ATOM 296 N ALA 1 10.883 6.779 -6.464 1.00 0.00 N ATOM 297 CA ALA 1 11.451 6.531 -5.142 1.00 0.00 C ... ... ATOM 588 1HG GLU 18 -13.363 -4.163 -2.372 1.00 0.00 H ATOM 589 2HG GLU 18 -12.634 -3.023 -3.475 1.00 0.00 H TER 590 GLU 18 ENDMDL ATOMOverviewThe ATOM records present the atomic coordinates for standard residues (see http://deposit.pdb.org/public-component-erf.cif). They also present the occupancy and temperature factor for each atom. Heterogen coordinates use the HETATM record type. The element symbol is always present on each ATOM record; segment identifier and charge are optional. 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
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.
PDB checks ATOM/HETATM records for PDB format, sequence information, and packing. The PDB reserves the right to return deposited coordinates to the author for transformation into PDB format. Relationships to Other Record TypesThe ATOM records are compared to the corresponding sequence database. Residue 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 145 N VAL A 25 32.433 16.336 57.540 1.00 11.92 N ATOM 146 CA VAL A 25 31.132 16.439 58.160 1.00 11.85 C ATOM 147 C VAL A 25 30.447 15.105 58.363 1.00 12.34 C ATOM 148 O VAL A 25 29.520 15.059 59.174 1.00 15.65 O ATOM 149 CB AVAL A 25 30.385 17.437 57.230 0.28 13.88 C ATOM 150 CB BVAL A 25 30.166 17.399 57.373 0.72 15.41 C ATOM 151 CG1AVAL A 25 28.870 17.401 57.336 0.28 12.64 C ATOM 152 CG1BVAL A 25 30.805 18.788 57.449 0.72 15.11 C ATOM 153 CG2AVAL A 25 30.835 18.826 57.661 0.28 13.58 C ATOM 154 CG2BVAL A 25 29.909 16.996 55.922 0.72 13.25 CKnown Problems No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U). SIGATMOverviewThe SIGATM records present the standard deviation of atomic parameters as they appear in ATOM and HETATM records. Record Format
COLUMNS DATA TYPE FIELD DEFINITION ----------------------------------------------------------------------- 1 - 6 Record name "SIGATM" 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. 31 - 38 Real(8.3) sigX Standard deviations of the stored coordinates (Angstroms). 39 - 46 Real(8.3) sigY Standard deviations of the stored coordinates (Angstroms). 47 - 54 Real(8.3) sigZ Standard deviations of the stored coordinates (Angstroms). 55 - 60 Real(6.2) sigOcc Standard deviation of occupancy. 61 - 66 Real(6.2) sigTemp Standard deviation of temperature factor. 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom.Details
The depositor provides SIGATM records, PDB verifies their format. Relationships to Other Record TypesSIGATM is related to the immediately preceding ATOM/HETATM record. Example
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 ATOM 230 N PRO 15 20.860 29.640 13.460 1.00 12.20 N SIGATM 230 N PRO 15 0.040 0.030 0.030 0.00 0.00 N ATOM 231 CA PRO 15 22.180 29.010 12.960 1.00 14.70 C SIGATM 231 CA PRO 15 0.060 0.040 0.050 0.00 0.00 C ATOM 232 C PRO 15 23.170 30.090 12.670 1.00 19.10 C SIGATM 232 C PRO 15 0.080 0.070 0.060 0.00 0.00 C ATOM 233 O PRO 15 24.360 29.860 12.670 1.00 17.50 O SIGATM 233 O PRO 15 0.040 0.030 0.030 0.00 0.00 O ATOM 234 CB PRO 15 21.710 28.220 11.640 1.00 17.70 C SIGATM 234 CB PRO 15 0.060 0.040 0.050 0.00 0.00 C ATOM 235 CG PRO 15 20.470 28.710 11.590 1.00 23.90 C SIGATM 235 CG PRO 15 0.080 0.060 0.060 0.00 0.00 C ATOM 236 CD PRO 15 19.640 29.320 12.660 1.00 15.50 C SIGATM 236 CD PRO 15 0.060 0.040 0.050 0.00 0.00 C ATOM 237 HA PRO 15 22.630 28.400 13.620 1.00 14.70 H ATOM 238 1HB PRO 15 22.240 28.540 10.860 1.00 17.70 H ATOM 239 2HB PRO 15 21.670 27.240 11.840 1.00 17.70 H ATOM 240 1HG PRO 15 20.360 29.240 10.740 1.00 23.90 H ATOM 241 2HG PRO 15 19.900 28.120 11.020 1.00 23.90 H ATOM 242 1HD PRO 15 19.230 30.160 12.320 1.00 15.50 H ATOM 243 2HD PRO 15 19.120 28.600 13.120 1.00 15.50 H ANISOUOverviewThe 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
The depositor provides ANISOU records, and the PDB verifies their format. Relationships to Other Record TypesThe 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 13 12.681 37.302 -25.211 1.000 15.56 N ANISOU 107 N GLY 13 2406 1892 1614 198 519 -328 N ATOM 108 CA GLY 13 11.982 37.996 -26.241 1.000 16.92 C ANISOU 108 CA GLY 13 2748 2004 1679 -21 155 -419 C ATOM 109 C GLY 13 11.678 39.447 -26.008 1.000 15.73 C ANISOU 109 C GLY 13 2555 1955 1468 87 357 -109 C ATOM 110 O GLY 13 11.444 40.201 -26.971 1.000 20.93 O ANISOU 110 O GLY 13 3837 2505 1611 164 -121 189 O ATOM 111 N ASN 14 11.608 39.863 -24.755 1.000 13.68 N ANISOU 111 N ASN 14 2059 1674 1462 27 244 -96 N SIGUIJOverviewThe SIGUIJ records present the standard deviations of anisotropic temperature factors scaled by a factor of 10**4 (Angstroms**2). Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------ 1 - 6 Record name "SIGUIJ" 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 sig[1][1] Sigma U(1,1) 36 - 42 Integer sig[2][2] Sigma U(2,2) 43 - 49 Integer sig[3][3] Sigma U(3,3) 50 - 56 Integer sig[1][2] Sigma U(1,2) 57 - 63 Integer sig[1][3] Sigma U(1,3) 64 - 70 Integer sig[2][3] Sigma U(2,3) 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom.Details
The depositor provides SIGUIJ records, PDB verifies their format. Relationships to Other Record TypesThe 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 13 12.681 37.302 -25.211 1.000 15.56 N ANISOU 107 N GLY 13 2406 1892 1614 198 519 -328 N SIGUIJ 107 N GLY 13 10 10 10 10 10 10 N ATOM 108 CA GLY 13 11.982 37.996 -26.241 1.000 16.92 C ANISOU 108 CA GLY 13 2748 2004 1679 -21 155 -419 C SIGUIJ 108 CA GLY 13 10 10 10 10 10 10 C ATOM 109 C GLY 13 11.678 39.447 -26.008 1.000 15.73 C ANISOU 109 C GLY 13 2555 1955 1468 87 357 -109 C SIGUIJ 109 C GLY 13 10 10 10 10 10 10 C ATOM 110 O GLY 13 11.444 40.201 -26.971 1.000 20.93 O ANISOU 110 O GLY 13 3837 2505 1611 164 -121 189 O SIGUIJ 110 O GLY 13 10 10 10 10 10 10 O ATOM 111 N ASN 14 11.608 39.863 -24.755 1.000 13.68 N ANISOU 111 N ASN 14 2059 1674 1462 27 244 -96 N SIGUIJ 111 N ASN 14 10 10 10 10 10 10 N TEROverviewThe 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
TER must appear at the end carboxy or 3' 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 TypesThe 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 4150 H ALA A 431 8.674 16.036 12.858 1.00 0.00 H TER 4151 ALA A 431 ATOM 1403 O PRO P 22 12.701 33.564 15.827 1.09 18.03 O ATOM 1404 CB PRO P 22 13.512 32.617 18.642 1.09 9.32 C ATOM 1405 CG PRO P 22 12.828 33.382 19.740 1.09 12.23 C ATOM 1406 CD PRO P 22 12.324 34.603 18.985 1.09 11.47 C HETATM 1407 CA BLE P 1 14.625 32.240 14.151 1.09 16.76 C HETATM 1408 CB BLE P 1 15.610 33.091 13.297 1.09 16.56 C HETATM 1409 CG BLE P 1 15.558 34.629 13.373 1.09 14.27 C HETATM 1410 CD1 BLE P 1 16.601 35.208 12.440 1.09 14.75 C HETATM 1411 CD2 BLE P 1 14.209 35.160 12.930 1.09 15.60 C HETATM 1412 N BLE P 1 14.777 32.703 15.531 1.09 14.79 N HETATM 1413 B BLE P 1 14.921 30.655 14.194 1.09 15.56 B HETATM 1414 O1 BLE P 1 14.852 30.178 12.832 1.09 16.10 O HETATM 1415 O2 BLE P 1 13.775 30.147 14.862 1.09 20.95 O TER 1416 BLE P 1 HETATMOverviewThe HETATM records present the atomic coordinate records for atoms within "non-standard" groups. These records are used for water molecules and atoms presented in HET groups (see http://deposit.pdb.org/public-component-erf.cif). 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
PDB processing programs check ATOM/HETATM records for PDB format, sequence information, and packing. The PDB reserves the right to return deposited coordinates to the author for transformation into PDB format. Relationships to Other Record TypesHETATM records must have corresponding HET, HETNAM, FORMUL and CONECT records, except for waters. Example
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 HETATM 1357 MG MG 168 4.669 34.118 19.123 1.00 3.16 MG2+ HETATM 3835 FE HEM 1 17.140 3.115 15.066 1.00 14.14 FE3+ ENDMDLOverviewThe 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
Entries with multiple structures in the EXPDTA record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models. Relationships to Other Record TypesThere must be a corresponding MODEL record. In the case of an NMR entry the EXPDTA 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 MODEL 10 ATOM 16372 N SER 1 -22.285 7.041 10.003 1.00 0.00 N ATOM 16373 CA SER 1 -23.026 6.872 8.720 1.00 0.00 C ... ... ATOM 18188 1HG GLU 122 -1.467 18.282 -17.144 1.00 0.00 H ATOM 18189 2HG GLU 122 -2.711 18.067 -15.913 1.00 0.00 H TER 18190 GLU 122 ENDMDL |