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AL2TS translates sequence - structure alignment (AL format) into standard PDB atom records (TS format). Document describes the format required to use the AL2TS facility.
PARENT - Specifies PDB entry used by AL model TER - Terminates independent segments of structure in the AL model
AL - Format to express unambiguous ALignments to PDB entries TS - 3D atomic coordinates (Tertiary Structure) PDB format
AL model should begin with a single PARENT record and terminate with a TER record. The (four column) alignment data records provide: model residue name (one letter symbol), model residue sequence number, PDB residue name (one letter symbol), and PDB residue sequence number with an insertion code if necessary:
aa1 n1 aa2 n2
Note:
- no model residue may be repeated in the alignment
- if a chain ID has to be specified in the PDB atom records, then
the model residue sequence number should be composed of a chain ID
and residue number, e.g. A2, B44
- only one chain ID specification for the model can be used in the
alignment
Record PARENT indicates structure templates used to generate any independent segment of AL model. The PARENT record should be placed as the first record of any such independent segment. Only one PARENT record per structure segment is allowed. The PDB code with chain extension of the structure the alignment is based on should be placed in the PARENT record.
PARENT mabc_A
Indicates that the model or the independent segment of structure is
based on a single PDB entry mabc chain A (use _A to indicate chain A).
Note that, the code must correspond to a current PDB entry.
Record TER is used to terminate an independent segment of structure.
TER
AL2TS translates AL format into standard PDB atom records (TS format).
Notes:
- by default atoms contain "1.0" in the occupancy field
- by default atoms contain "0.0" in the temperature factor field
- only N, CA, C, and O atoms are reported
PARENT 1ppf_E S 5 V 62 Q 6 N 63 T 7 V 63A C 8 R 63B Y 9 A 63C N 10 V 64 S 11 R 65 TER PARENT 1bdb E 17 L 249 T 18 N 250 V 19 Y 251 D 20 D 252 G 21 G 253 R 22 G 254 A 23 L 255 L 24 G 256 K 25 V 257 TER
TS model (output)
Alignments (AL model) will be converted into a 3D structures (TS format).
REMARK Coordinates assigned from PDB entry: 1ppf_E ATOM 1 N SER 5 18.705 68.098 12.470 1.00 0.00 ATOM 2 CA SER 5 19.570 69.255 12.136 1.00 0.00 ATOM 3 C SER 5 18.647 70.218 11.461 1.00 0.00 ATOM 4 O SER 5 17.566 69.796 11.034 1.00 0.00 ATOM 5 N GLN 6 19.056 71.460 11.446 1.00 0.00 ATOM 6 CA GLN 6 18.313 72.496 10.743 1.00 0.00 ATOM 7 C GLN 6 18.742 72.528 9.250 1.00 0.00 ATOM 8 O GLN 6 19.833 73.029 8.938 1.00 0.00 ATOM 9 N THR 7 17.949 71.827 8.408 1.00 0.00 ATOM 10 CA THR 7 18.209 71.711 6.952 1.00 0.00 ATOM 11 C THR 7 18.385 73.033 6.242 1.00 0.00 ATOM 12 O THR 7 19.189 73.137 5.309 1.00 0.00 ATOM 13 N CYS 8 17.707 74.044 6.731 1.00 0.00 ATOM 14 CA CYS 8 17.914 75.435 6.180 1.00 0.00 ATOM 15 C CYS 8 19.353 75.926 6.329 1.00 0.00 ATOM 16 O CYS 8 19.693 76.899 5.658 1.00 0.00 ATOM 17 N TYR 9 20.109 75.389 7.300 1.00 0.00 ATOM 18 CA TYR 9 21.520 75.885 7.551 1.00 0.00 ATOM 19 C TYR 9 22.542 75.098 6.714 1.00 0.00 ATOM 20 O TYR 9 23.731 75.385 6.826 1.00 0.00 ATOM 21 N ASN 10 22.068 74.026 6.012 1.00 0.00 ATOM 22 CA ASN 10 23.072 73.133 5.413 1.00 0.00 ATOM 23 C ASN 10 23.523 73.680 4.096 1.00 0.00 ATOM 24 O ASN 10 22.692 74.294 3.454 1.00 0.00 ATOM 25 N SER 11 24.773 73.859 3.896 1.00 0.00 ATOM 26 CA SER 11 25.276 74.259 2.536 1.00 0.00 ATOM 27 C SER 11 25.789 73.003 1.827 1.00 0.00 ATOM 28 O SER 11 26.284 72.058 2.468 1.00 0.00 REMARK Coordinates assigned from PDB entry: 1bdb ATOM 29 N GLU 17 28.577 65.212 0.633 1.00 0.00 ATOM 30 CA GLU 17 28.012 66.107 1.638 1.00 0.00 ATOM 31 C GLU 17 28.404 65.702 3.062 1.00 0.00 ATOM 32 O GLU 17 27.936 64.662 3.546 1.00 0.00 ATOM 33 N THR 18 29.230 66.499 3.734 1.00 0.00 ATOM 34 CA THR 18 29.517 66.231 5.144 1.00 0.00 ATOM 35 C THR 18 28.241 66.516 5.952 1.00 0.00 ATOM 36 O THR 18 27.643 67.584 5.886 1.00 0.00 ATOM 37 N VAL 19 27.835 65.524 6.722 1.00 0.00 ATOM 38 CA VAL 19 26.533 65.570 7.383 1.00 0.00 ATOM 39 C VAL 19 26.565 64.886 8.730 1.00 0.00 ATOM 40 O VAL 19 25.837 63.936 8.950 1.00 0.00 ATOM 41 N ASP 20 27.464 65.351 9.615 1.00 0.00 ATOM 42 CA ASP 20 27.768 64.585 10.812 1.00 0.00 ATOM 43 C ASP 20 27.711 65.444 12.054 1.00 0.00 ATOM 44 O ASP 20 28.262 65.055 13.081 1.00 0.00 ATOM 45 N GLY 21 27.143 66.659 11.942 1.00 0.00 ATOM 46 CA GLY 21 27.082 67.541 13.112 1.00 0.00 ATOM 47 C GLY 21 28.239 68.535 13.138 1.00 0.00 ATOM 48 O GLY 21 28.303 69.340 14.078 1.00 0.00 ATOM 49 N ARG 22 29.040 68.583 12.066 1.00 0.00 ATOM 50 CA ARG 22 30.105 69.584 12.033 1.00 0.00 ATOM 51 C ARG 22 31.453 69.120 12.545 1.00 0.00 ATOM 52 O ARG 22 32.328 69.950 12.865 1.00 0.00 ATOM 53 N ALA 23 31.693 67.798 12.593 1.00 0.00 ATOM 54 CA ALA 23 33.014 67.356 13.076 1.00 0.00 ATOM 55 C ALA 23 34.174 68.035 12.370 1.00 0.00 ATOM 56 O ALA 23 35.212 68.317 12.985 1.00 0.00 ATOM 57 N LEU 24 34.083 68.218 11.048 1.00 0.00 ATOM 58 CA LEU 24 35.146 68.831 10.275 1.00 0.00 ATOM 59 C LEU 24 35.366 70.310 10.547 1.00 0.00 ATOM 60 O LEU 24 36.423 70.816 10.155 1.00 0.00 ATOM 61 N LYS 25 34.430 71.013 11.215 1.00 0.00 ATOM 62 CA LYS 25 34.663 72.409 11.528 1.00 0.00 ATOM 63 C LYS 25 34.709 72.637 13.036 1.00 0.00 ATOM 64 O LYS 25 34.553 73.764 13.493 1.00 0.00 END
PARENT 1aaq_B M A21 V 11 P A22 T 12 A A25 I 13 P A32 A 22 N A33 L 23 TER
TS model (output)
Alignments (AL model) will be converted into a 3D structures (TS format)
with chain name of 'A'.
REMARK Coordinates assigned from PDB entry: 1aaq_B ATOM 1 N MET A 21 -4.518 31.697 3.131 1.00 0.00 ATOM 2 CA MET A 21 -4.532 32.774 4.132 1.00 0.00 ATOM 3 C MET A 21 -3.275 32.642 5.046 1.00 0.00 ATOM 4 O MET A 21 -2.579 31.635 5.060 1.00 0.00 ATOM 5 N PRO A 22 -2.834 33.586 5.842 1.00 0.00 ATOM 6 CA PRO A 22 -1.691 33.474 6.749 1.00 0.00 ATOM 7 C PRO A 22 -2.154 33.233 8.196 1.00 0.00 ATOM 8 O PRO A 22 -3.099 33.897 8.682 1.00 0.00 ATOM 9 N ALA A 25 -1.566 32.240 8.872 1.00 0.00 ATOM 10 CA ALA A 25 -1.952 31.974 10.259 1.00 0.00 ATOM 11 C ALA A 25 -0.751 32.284 11.167 1.00 0.00 ATOM 12 O ALA A 25 0.385 32.224 10.665 1.00 0.00 ATOM 13 N PRO A 32 -2.228 28.583 5.108 1.00 0.00 ATOM 14 CA PRO A 32 -3.235 27.537 5.200 1.00 0.00 ATOM 15 C PRO A 32 -4.353 27.738 4.178 1.00 0.00 ATOM 16 O PRO A 32 -4.626 28.850 3.748 1.00 0.00 ATOM 17 N ASN A 33 -4.994 26.694 3.758 1.00 0.00 ATOM 18 CA ASN A 33 -6.019 26.691 2.748 1.00 0.00 ATOM 19 C ASN A 33 -7.383 26.690 3.455 1.00 0.00 ATOM 20 O ASN A 33 -7.605 25.781 4.243 1.00 0.00 END
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