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Various PDB fixes (#87)
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Fixes #68
* remove ANISOU records
* HETATM caps, remove NMA icodes
* NMA to NME, fix cap hydrogen names
* Remove cap CONECT records
* fix hydrogen naming for ace bonded terminal AAs
* move pde2 ion connections to LINK section
* move ion coordination bonds to LINK section
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@IAlibay
IAlibay authored Feb 7, 2023
1 parent e9b153e commit d338760
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68 changes: 30 additions & 38 deletions data/cdk2/01_protein/crd/protein.pdb
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ SEQRES 19 A 299 MET PRO ASP TYR LYS PRO SER PHE PRO LYS TRP ALA ARG
SEQRES 20 A 299 GLN ASP PHE SER LYS VAL VAL PRO PRO LEU ASP GLU ASP
SEQRES 21 A 299 GLY ARG SER LEU LEU SER GLN MET LEU HIS TYR ASP PRO
SEQRES 22 A 299 ASN LYS ARG ILE SER ALA LYS ALA ALA LEU ALA HIS PRO
SEQRES 23 A 299 PHE PHE GLN ASP VAL THR LYS PRO VAL PRO HIS LEU NMA
SEQRES 23 A 299 PHE PHE GLN ASP VAL THR LYS PRO VAL PRO HIS LEU NME
SEQRES 1 B 260 ACE VAL PRO ASP TYR HIS GLU ASP ILE HIS THR TYR LEU
SEQRES 2 B 260 ARG GLU MET GLU VAL LYS CYS LYS PRO LYS VAL GLY TYR
SEQRES 3 B 260 MET LYS LYS GLN PRO ASP ILE THR ASN SER MET ARG ALA
Expand All @@ -62,7 +62,7 @@ SEQRES 16 B 260 GLY GLN SER TRP PRO GLU SER LEU ILE ARG LYS THR GLY
SEQRES 17 B 260 TYR THR LEU GLU SER LEU LYS PRO CYS LEU MET ASP LEU
SEQRES 18 B 260 HIS GLN THR TYR LEU LYS ALA PRO GLN HIS ALA GLN GLN
SEQRES 19 B 260 SER ILE ARG GLU LYS TYR LYS ASN SER LYS TYR HIS GLY
SEQRES 20 B 260 VAL SER LEU LEU ASN PRO PRO GLU THR LEU ASN LEU NMA
SEQRES 20 B 260 VAL SER LEU LEU ASN PRO PRO GLU THR LEU ASN LEU NME
FORMUL 3 HOH *(H2 0)
HELIX 1 1 THR A 47 THR A 47 1
HELIX 2 2 ALA A 48 ALA A 48 1
Expand Down Expand Up @@ -620,19 +620,19 @@ SHEET 1 47 1 LEU A 143 LEU A 143 0
SHEET 1 48 1 ARG A 150 ARG A 150 0
SHEET 1 49 1 ALA A 151 ALA A 151 0
CRYST1 73.990 134.730 148.120 90.00 90.00 90.00 P 21 21 21 8
ATOM 1 CH3 ACE A -1 16.172 62.928 36.854 1.00 0.00 C
ATOM 2 C ACE A -1 16.053 62.130 38.147 1.00 0.00 C
ATOM 3 O ACE A -1 16.818 61.193 38.371 1.00 0.00 O
ATOM 4 1H ACE A -1 17.075 62.644 36.315 1.00 0.00 H
ATOM 5 2H ACE A -1 15.310 62.781 36.207 1.00 0.00 H
ATOM 6 3H ACE A -1 16.246 63.993 37.078 1.00 0.00 H
HETATM 1 CH3 ACE A -1 16.172 62.928 36.854 1.00 0.00 C
HETATM 2 C ACE A -1 16.053 62.130 38.147 1.00 0.00 C
HETATM 3 O ACE A -1 16.818 61.193 38.371 1.00 0.00 O
HETATM 4 H1 ACE A -1 17.075 62.644 36.315 1.00 0.00 H
HETATM 5 H2 ACE A -1 15.310 62.781 36.207 1.00 0.00 H
HETATM 6 H3 ACE A -1 16.246 63.993 37.078 1.00 0.00 H
ATOM 7 N SER A 0 15.118 62.550 39.012 1.00 68.83 N
ATOM 8 CA SER A 0 15.041 62.142 40.416 1.00 69.08 C
ATOM 9 C SER A 0 14.518 60.706 40.618 1.00 69.23 C
ATOM 10 O SER A 0 15.264 59.867 41.121 1.00 68.19 O
ATOM 11 CB SER A 0 14.237 63.205 41.189 1.00 67.84 C
ATOM 12 OG SER A 0 14.298 62.986 42.583 1.00 65.82 O
ATOM 13 H1 SER A 0 14.516 63.315 38.746 1.00 68.83 H
ATOM 13 H SER A 0 14.516 63.315 38.746 1.00 68.83 H
ATOM 14 HA SER A 0 16.060 62.167 40.810 1.00 69.08 H
ATOM 15 HB3 SER A 0 13.194 63.222 40.872 1.00 67.84 H
ATOM 16 HB2 SER A 0 14.642 64.199 40.995 1.00 67.84 H
Expand Down Expand Up @@ -5442,27 +5442,27 @@ ATOM 4819 HD13 LEU A 296 8.630 32.957 46.590 1.00179.04 H
ATOM 4820 HD21 LEU A 296 6.527 32.346 47.123 1.00179.08 H
ATOM 4821 HD22 LEU A 296 5.987 31.387 45.758 1.00179.08 H
ATOM 4822 HD23 LEU A 296 6.029 30.688 47.371 1.00179.08 H
ATOM 4823 N NMA A 296A 6.225 28.917 42.557 1.00 0.00 N
ATOM 4824 CA NMA A 296A 6.044 28.689 41.129 1.00 0.00 C
ATOM 4825 H NMA A 296A 5.424 29.264 43.066 1.00 0.00 H
ATOM 4826 1HA NMA A 296A 6.973 28.448 40.611 1.00 0.00 H
ATOM 4827 2HA NMA A 296A 5.346 27.867 40.972 1.00 0.00 H
ATOM 4828 3HA NMA A 296A 5.626 29.582 40.665 1.00 0.00 H
TER 4829 NMA A 296A
ATOM 4830 CH3 ACE B 174 15.199 47.481 82.406 1.00 0.00 C
ATOM 4831 C ACE B 174 15.511 46.447 81.334 1.00 0.00 C
ATOM 4832 O ACE B 174 15.941 46.814 80.242 1.00 0.00 O
ATOM 4833 1H ACE B 174 16.112 48.012 82.676 1.00 0.00 H
ATOM 4834 2H ACE B 174 14.471 48.202 82.034 1.00 0.00 H
ATOM 4835 3H ACE B 174 14.794 47.021 83.308 1.00 0.00 H
HETATM 4823 N NME A 297 6.225 28.917 42.557 1.00 0.00 N
HETATM 4824 C NME A 297 6.044 28.689 41.129 1.00 0.00 C
HETATM 4825 H NME A 297 5.424 29.264 43.066 1.00 0.00 H
HETATM 4826 H1 NME A 297 6.973 28.448 40.611 1.00 0.00 H
HETATM 4827 H2 NME A 297 5.346 27.867 40.972 1.00 0.00 H
HETATM 4828 H3 NME A 297 5.626 29.582 40.665 1.00 0.00 H
TER 4829 NME A 297
HETATM 4830 CH3 ACE B 174 15.199 47.481 82.406 1.00 0.00 C
HETATM 4831 C ACE B 174 15.511 46.447 81.334 1.00 0.00 C
HETATM 4832 O ACE B 174 15.941 46.814 80.242 1.00 0.00 O
HETATM 4833 H1 ACE B 174 16.112 48.012 82.676 1.00 0.00 H
HETATM 4834 H2 ACE B 174 14.471 48.202 82.034 1.00 0.00 H
HETATM 4835 H3 ACE B 174 14.794 47.021 83.308 1.00 0.00 H
ATOM 4836 N VAL B 175 15.312 45.161 81.671 1.00124.49 N
ATOM 4837 CA VAL B 175 15.623 43.985 80.850 1.00123.90 C
ATOM 4838 C VAL B 175 17.152 43.853 80.557 1.00120.75 C
ATOM 4839 O VAL B 175 17.612 44.204 79.470 1.00120.70 O
ATOM 4840 CB VAL B 175 14.642 43.866 79.620 1.00125.35 C
ATOM 4841 CG1 VAL B 175 15.195 43.532 78.223 1.00125.65 C
ATOM 4842 CG2 VAL B 175 13.495 42.891 79.951 1.00125.73 C
ATOM 4843 H2 VAL B 175 14.943 44.956 82.588 1.00124.49 H
ATOM 4843 H VAL B 175 14.943 44.956 82.588 1.00124.49 H
ATOM 4844 HA VAL B 175 15.389 43.135 81.491 1.00123.90 H
ATOM 4845 HB VAL B 175 14.154 44.832 79.489 1.00125.35 H
ATOM 4846 HG11 VAL B 175 14.377 43.399 77.522 1.00125.65 H
Expand Down Expand Up @@ -9646,20 +9646,16 @@ ATOM 9023 HD13 LEU B 432 37.547 63.801 90.177 1.00143.31 H
ATOM 9024 HD21 LEU B 432 37.226 62.697 92.118 1.00143.39 H
ATOM 9025 HD22 LEU B 432 38.939 62.501 92.485 1.00143.39 H
ATOM 9026 HD23 LEU B 432 37.834 63.178 93.682 1.00143.39 H
ATOM 9027 N NMA B 432A 42.829 64.775 92.800 1.00 0.00 N
ATOM 9028 CA NMA B 432A 44.202 65.238 92.661 1.00 0.00 C
ATOM 9029 H NMA B 432A 42.569 63.934 92.304 1.00 0.00 H
ATOM 9030 1HA NMA B 432A 44.686 65.324 93.635 1.00 0.00 H
ATOM 9031 2HA NMA B 432A 44.774 64.531 92.060 1.00 0.00 H
ATOM 9032 3HA NMA B 432A 44.237 66.211 92.170 1.00 0.00 H
TER 9033 NMA B 432A
HETATM 9027 N NME B 434 42.829 64.775 92.800 1.00 0.00 N
HETATM 9028 C NME B 434 44.202 65.238 92.661 1.00 0.00 C
HETATM 9029 H NME B 434 42.569 63.934 92.304 1.00 0.00 H
HETATM 9030 H1 NME B 434 44.686 65.324 93.635 1.00 0.00 H
HETATM 9031 H2 NME B 434 44.774 64.531 92.060 1.00 0.00 H
HETATM 9032 H3 NME B 434 44.237 66.211 92.170 1.00 0.00 H
TER 9033 NME B 434
HETATM 9034 O HOH A2117 9.269 47.894 54.897 1.00 28.52 O
HETATM 9035 H1 HOH A2117 9.288 47.518 53.968 1.00 28.52 H
HETATM 9036 H2 HOH A2117 9.994 48.578 54.995 1.00 28.52 H
CONECT 1 4 5 6
CONECT 4 1
CONECT 5 1
CONECT 6 1
CONECT 2618 2599 2619 2629
CONECT 2619 2618 2620 2627 2630
CONECT 2620 2619 2621 2622 2631
Expand All @@ -9677,10 +9673,6 @@ CONECT 2631 2620
CONECT 2632 2621
CONECT 2633 2621
CONECT 2634 2621
CONECT 4830 4833 4834 4835
CONECT 4833 4830
CONECT 4834 4830
CONECT 4835 4830
CONECT 9034 9035 9036
CONECT 9035 9034
CONECT 9036 9034
Expand Down
66 changes: 29 additions & 37 deletions data/cdk8/01_protein/crd/protein.pdb
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ SEQRES 24 A 364 TYR MET GLU LYS HIS LYS VAL LYS PRO ASP SER LYS ALA
SEQRES 25 A 364 PHE HIS LEU LEU GLN LYS LEU LEU THR MET ASP PRO ILE
SEQRES 26 A 364 LYS ARG ILE THR SER GLU GLN ALA MET GLN ASP PRO TYR
SEQRES 27 A 364 PHE LEU GLU ASP PRO LEU PRO THR SER ASP VAL PHE ALA
SEQRES 28 A 364 GLY CYS GLN ILE PRO TYR PRO LYS ARG GLU PHE LEU NMA
SEQRES 28 A 364 GLY CYS GLN ILE PRO TYR PRO LYS ARG GLU PHE LEU NME
SEQRES 1 B 268 ACE LYS ALA MET ALA GLY ASN PHE TRP GLN SER SER HIS
SEQRES 2 B 268 TYR LEU GLN TRP ILE LEU ASP LYS GLN ASP LEU LEU LYS
SEQRES 3 B 268 GLU ARG GLN LYS ASP LEU LYS PHE LEU SER GLU GLU GLU
Expand All @@ -64,7 +64,7 @@ SEQRES 17 B 268 CYS VAL VAL GLN GLN LYS ASP ALA ARG GLN TRP PHE ALA
SEQRES 18 B 268 GLU LEU SER VAL ASP MET GLU LYS ILE LEU GLU ILE ILE
SEQRES 19 B 268 ARG VAL ILE LEU LYS LEU TYR GLU GLN TRP LYS ASN PHE
SEQRES 20 B 268 ASP GLU ARG LYS GLU MET ALA THR ILE LEU SER LYS MET
SEQRES 21 B 268 PRO LYS PRO LYS PRO PRO PRO NMA
SEQRES 21 B 268 PRO LYS PRO LYS PRO PRO PRO NME
HELIX 1 1 TYR A 3 TYR A 3 1
HELIX 2 2 ASP A 4 ASP A 4 1
HELIX 3 3 PHE A 5 PHE A 5 1
Expand Down Expand Up @@ -696,12 +696,12 @@ SHEET 1 39 1 VAL A 169 VAL A 169 0
SHEET 1 40 1 LYS A 170 LYS A 170 0
SHEET 1 41 1 ILE A 171 ILE A 171 0
CRYST1 71.232 71.439 171.000 90.00 90.00 90.00 P 21 21 21 4
ATOM 1 CH3 ACE A -3 -27.867 31.795 -24.072 1.00 0.00 C
ATOM 2 C ACE A -3 -28.241 32.500 -25.369 1.00 0.00 C
ATOM 3 O ACE A -3 -28.700 31.841 -26.297 1.00 0.00 O
ATOM 4 1H ACE A -3 -28.476 30.903 -23.930 1.00 0.00 H
ATOM 5 2H ACE A -3 -26.825 31.481 -24.113 1.00 0.00 H
ATOM 6 3H ACE A -3 -27.995 32.448 -23.208 1.00 0.00 H
HETATM 1 CH3 ACE A -3 -27.867 31.795 -24.072 1.00 0.00 C
HETATM 2 C ACE A -3 -28.241 32.500 -25.369 1.00 0.00 C
HETATM 3 O ACE A -3 -28.700 31.841 -26.297 1.00 0.00 O
HETATM 4 H1 ACE A -3 -28.476 30.903 -23.930 1.00 0.00 H
HETATM 5 H2 ACE A -3 -26.825 31.481 -24.113 1.00 0.00 H
HETATM 6 H3 ACE A -3 -27.995 32.448 -23.208 1.00 0.00 H
ATOM 7 N ASP A -2 -28.027 33.829 -25.409 1.00 99.89 N
ATOM 8 CA ASP A -2 -28.144 34.736 -26.563 1.00 99.82 C
ATOM 9 C ASP A -2 -29.605 34.995 -27.004 1.00 98.93 C
Expand All @@ -710,7 +710,7 @@ ATOM 11 CB ASP A -2 -27.239 34.282 -27.748 1.00 99.99 C
ATOM 12 CG ASP A -2 -27.014 35.262 -28.917 1.00102.11 C
ATOM 13 OD1 ASP A -2 -27.119 36.491 -28.705 1.00104.87 O
ATOM 14 OD2 ASP A -2 -26.612 34.772 -29.996 1.00102.65 O1-
ATOM 15 H2 ASP A -2 -27.658 34.267 -24.578 1.00 99.89 H
ATOM 15 H ASP A -2 -27.658 34.267 -24.578 1.00 99.89 H
ATOM 16 HA ASP A -2 -27.752 35.683 -26.189 1.00 99.82 H
ATOM 17 HB3 ASP A -2 -27.640 33.353 -28.146 1.00 99.99 H
ATOM 18 HB2 ASP A -2 -26.257 34.013 -27.357 1.00 99.99 H
Expand Down Expand Up @@ -6662,19 +6662,19 @@ ATOM 5963 HD13 LEU A 359 -7.116 15.944 -0.264 1.00 84.28 H
ATOM 5964 HD21 LEU A 359 -4.797 19.157 -0.760 1.00 84.51 H
ATOM 5965 HD22 LEU A 359 -5.561 18.025 -1.866 1.00 84.51 H
ATOM 5966 HD23 LEU A 359 -6.405 19.476 -1.384 1.00 84.51 H
ATOM 5967 N NMA A 359A -9.469 19.632 3.144 1.00 0.00 N
ATOM 5968 CA NMA A 359A -10.490 20.548 3.639 1.00 0.00 C
ATOM 5969 H NMA A 359A -8.573 19.659 3.609 1.00 0.00 H
ATOM 5970 1HA NMA A 359A -11.453 20.433 3.138 1.00 0.00 H
ATOM 5971 2HA NMA A 359A -10.647 20.380 4.705 1.00 0.00 H
ATOM 5972 3HA NMA A 359A -10.160 21.578 3.505 1.00 0.00 H
TER 5973 NMA A 359A
ATOM 5974 CH3 ACE B -2 2.190 16.434 -34.527 1.00 0.00 C
ATOM 5975 C ACE B -2 1.940 14.947 -34.755 1.00 0.00 C
ATOM 5976 O ACE B -2 2.432 14.119 -33.992 1.00 0.00 O
ATOM 5977 1H ACE B -2 2.919 16.585 -33.730 1.00 0.00 H
ATOM 5978 2H ACE B -2 2.574 16.902 -35.433 1.00 0.00 H
ATOM 5979 3H ACE B -2 1.264 16.935 -34.243 1.00 0.00 H
HETATM 5967 N NME A 360 -9.469 19.632 3.144 1.00 0.00 N
HETATM 5968 C NME A 360 -10.490 20.548 3.639 1.00 0.00 C
HETATM 5969 H NME A 360 -8.573 19.659 3.609 1.00 0.00 H
HETATM 5970 H1 NME A 360 -11.453 20.433 3.138 1.00 0.00 H
HETATM 5971 H2 NME A 360 -10.647 20.380 4.705 1.00 0.00 H
HETATM 5972 H3 NME A 360 -10.160 21.578 3.505 1.00 0.00 H
TER 5973 NME A 360
HETATM 5974 CH3 ACE B -2 2.190 16.434 -34.527 1.00 0.00 C
HETATM 5975 C ACE B -2 1.940 14.947 -34.755 1.00 0.00 C
HETATM 5976 O ACE B -2 2.432 14.119 -33.992 1.00 0.00 O
HETATM 5977 H1 ACE B -2 2.919 16.585 -33.730 1.00 0.00 H
HETATM 5978 H2 ACE B -2 2.574 16.902 -35.433 1.00 0.00 H
HETATM 5979 H3 ACE B -2 1.264 16.935 -34.243 1.00 0.00 H
ATOM 5980 N LYS B -1 1.165 14.632 -35.809 1.00 63.18 N
ATOM 5981 CA LYS B -1 0.772 13.282 -36.254 1.00 62.35 C
ATOM 5982 C LYS B -1 -0.143 12.525 -35.263 1.00 59.65 C
Expand All @@ -6684,7 +6684,7 @@ ATOM 5985 CG LYS B -1 2.849 13.071 -37.790 1.00 67.85 C
ATOM 5986 CD LYS B -1 4.042 12.189 -38.187 0.00 67.10 C
ATOM 5987 CE LYS B -1 4.921 12.847 -39.263 0.00 67.32 C
ATOM 5988 NZ LYS B -1 6.060 11.990 -39.638 0.00 67.29 N1+
ATOM 5989 H2 LYS B -1 0.805 15.387 -36.372 1.00 63.18 H
ATOM 5989 H LYS B -1 0.805 15.387 -36.372 1.00 63.18 H
ATOM 5990 HA LYS B -1 0.165 13.433 -37.147 1.00 62.35 H
ATOM 5991 HB3 LYS B -1 1.680 11.456 -37.013 1.00 63.51 H
ATOM 5992 HB2 LYS B -1 2.642 12.251 -35.805 1.00 63.51 H
Expand Down Expand Up @@ -11147,18 +11147,10 @@ ATOM 10448 HG3 PRO B 264 -41.256 32.732 -23.858 1.00 92.68 H
ATOM 10449 HG2 PRO B 264 -40.731 32.641 -22.177 1.00 92.68 H
ATOM 10450 HD2 PRO B 264 -38.798 34.064 -22.666 1.00 92.40 H
ATOM 10451 HD3 PRO B 264 -38.940 33.031 -24.091 1.00 92.40 H
ATOM 10452 N NMA B 264A -40.026 37.206 -22.292 1.00 0.00 N
ATOM 10453 CA NMA B 264A -39.847 38.486 -21.624 1.00 0.00 C
ATOM 10454 H NMA B 264A -39.447 36.438 -21.986 1.00 0.00 H
ATOM 10455 1HA NMA B 264A -39.565 39.261 -22.337 1.00 0.00 H
ATOM 10456 2HA NMA B 264A -40.766 38.792 -21.122 1.00 0.00 H
ATOM 10457 3HA NMA B 264A -39.060 38.408 -20.875 1.00 0.00 H
CONECT 1 4 5 6
CONECT 4 1
CONECT 5 1
CONECT 6 1
CONECT 5974 5977 5978 5979
CONECT 5977 5974
CONECT 5978 5974
CONECT 5979 5974
HETATM10452 N NME B 265 -40.026 37.206 -22.292 1.00 0.00 N
HETATM10453 C NME B 265 -39.847 38.486 -21.624 1.00 0.00 C
HETATM10454 H NME B 265 -39.447 36.438 -21.986 1.00 0.00 H
HETATM10455 H1 NME B 265 -39.565 39.261 -22.337 1.00 0.00 H
HETATM10456 H2 NME B 265 -40.766 38.792 -21.122 1.00 0.00 H
HETATM10457 H3 NME B 265 -39.060 38.408 -20.875 1.00 0.00 H
END
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