data_1M54 # _model_server_result.job_id C3ldpFlNaI7hRMJ0RmC8eQ _model_server_result.datetime_utc '2024-11-27 22:18:25' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1m54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":1620}' # _entry.id 1M54 # _exptl.entry_id 1M54 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 102.01 _cell.angle_beta 101.53 _cell.angle_gamma 112.6 _cell.entry_id 1M54 _cell.length_a 85.74 _cell.length_b 85.626 _cell.length_c 97.082 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1M54 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,S,T 1 1 C,D,K,L,M,N,U,V 2 1 E,F,O,P,Q,R,W,X 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A NZ LYS 76 A LYS 119 1_555 G C4A PLP . A PLP 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 B NZ LYS 76 B LYS 119 1_555 I C4A PLP . B PLP 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.025 ? covale ? covale3 C NZ LYS 76 C LYS 119 1_555 K C4A PLP . C PLP 1310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.05 ? covale ? covale4 D NZ LYS 76 D LYS 119 1_555 M C4A PLP . D PLP 1410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale5 E NZ LYS 76 E LYS 119 1_555 O C4A PLP . E PLP 1510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale6 F NZ LYS 76 F LYS 119 1_555 Q C4A PLP . F PLP 1610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? metalc ? metalc1 A SG CYS 9 A CYS 52 1_555 H FE HEM . A HEM 1120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc2 A NE2 HIS 22 A HIS 65 1_555 H FE HEM . A HEM 1120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc3 B SG CYS 9 B CYS 52 1_555 J FE HEM . B HEM 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc4 B NE2 HIS 22 B HIS 65 1_555 J FE HEM . B HEM 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc5 C SG CYS 9 C CYS 52 1_555 L FE HEM . C HEM 1320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc6 C NE2 HIS 22 C HIS 65 1_555 L FE HEM . C HEM 1320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc7 D SG CYS 9 D CYS 52 1_555 N FE HEM . D HEM 1420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc8 D NE2 HIS 22 D HIS 65 1_555 N FE HEM . D HEM 1420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc9 E SG CYS 9 E CYS 52 1_555 P FE HEM . E HEM 1520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc10 E NE2 HIS 22 E HIS 65 1_555 P FE HEM . E HEM 1520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc11 F SG CYS 9 F CYS 52 1_555 R FE HEM . F HEM 1620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc12 F NE2 HIS 22 F HIS 65 1_555 R FE HEM . F HEM 1620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # _atom_sites.entry_id 1M54 _atom_sites.fract_transf_matrix[1][1] 0.011663 _atom_sites.fract_transf_matrix[1][2] 0.004854 _atom_sites.fract_transf_matrix[1][3] 0.004117 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01265 _atom_sites.fract_transf_matrix[2][3] 0.004197 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011076 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code G 2 PLP A 1 1110 1110 PLP PLP . H 3 HEM A 1 1120 1120 HEM HEM . I 2 PLP B 1 1210 1210 PLP PLP . J 3 HEM B 1 1220 1220 HEM HEM . K 2 PLP C 1 1310 1310 PLP PLP . L 3 HEM C 1 1320 1320 HEM HEM . M 2 PLP D 1 1410 1410 PLP PLP . N 3 HEM D 1 1420 1420 HEM HEM . O 2 PLP E 1 1510 1510 PLP PLP . P 3 HEM E 1 1520 1520 HEM HEM . Q 2 PLP F 1 1610 1610 PLP PLP . R 3 HEM F 1 1620 1620 HEM HEM . S 4 HOH A 1 1121 4 HOH HOH . S 4 HOH A 2 1122 10 HOH HOH . S 4 HOH A 3 1123 25 HOH HOH . S 4 HOH A 4 1124 28 HOH HOH . S 4 HOH A 5 1125 31 HOH HOH . S 4 HOH A 6 1126 38 HOH HOH . S 4 HOH A 7 1127 42 HOH HOH . S 4 HOH A 8 1128 52 HOH HOH . S 4 HOH A 9 1129 53 HOH HOH . S 4 HOH A 10 1130 62 HOH HOH . S 4 HOH A 11 1131 76 HOH HOH . S 4 HOH A 12 1132 87 HOH HOH . T 4 HOH B 1 1221 1 HOH HOH . T 4 HOH B 2 1222 6 HOH HOH . T 4 HOH B 3 1223 7 HOH HOH . T 4 HOH B 4 1224 11 HOH HOH . T 4 HOH B 5 1225 13 HOH HOH . T 4 HOH B 6 1226 30 HOH HOH . T 4 HOH B 7 1227 34 HOH HOH . T 4 HOH B 8 1228 60 HOH HOH . T 4 HOH B 9 1229 66 HOH HOH . T 4 HOH B 10 1230 70 HOH HOH . T 4 HOH B 11 1231 78 HOH HOH . T 4 HOH B 12 1232 89 HOH HOH . U 4 HOH C 1 1321 17 HOH HOH . U 4 HOH C 2 1322 22 HOH HOH . U 4 HOH C 3 1323 27 HOH HOH . U 4 HOH C 4 1324 29 HOH HOH . U 4 HOH C 5 1325 35 HOH HOH . U 4 HOH C 6 1326 37 HOH HOH . U 4 HOH C 7 1327 46 HOH HOH . U 4 HOH C 8 1328 51 HOH HOH . U 4 HOH C 9 1329 63 HOH HOH . U 4 HOH C 10 1330 72 HOH HOH . U 4 HOH C 11 1331 81 HOH HOH . U 4 HOH C 12 1332 91 HOH HOH . U 4 HOH C 13 1333 99 HOH HOH . U 4 HOH C 14 1334 100 HOH HOH . V 4 HOH D 1 1421 2 HOH HOH . V 4 HOH D 2 1422 5 HOH HOH . V 4 HOH D 3 1423 16 HOH HOH . V 4 HOH D 4 1424 21 HOH HOH . V 4 HOH D 5 1425 32 HOH HOH . V 4 HOH D 6 1426 36 HOH HOH . V 4 HOH D 7 1427 43 HOH HOH . V 4 HOH D 8 1428 44 HOH HOH . V 4 HOH D 9 1429 45 HOH HOH . V 4 HOH D 10 1430 50 HOH HOH . V 4 HOH D 11 1431 54 HOH HOH . V 4 HOH D 12 1432 58 HOH HOH . V 4 HOH D 13 1433 59 HOH HOH . V 4 HOH D 14 1434 67 HOH HOH . V 4 HOH D 15 1435 71 HOH HOH . V 4 HOH D 16 1436 74 HOH HOH . V 4 HOH D 17 1437 79 HOH HOH . V 4 HOH D 18 1438 80 HOH HOH . V 4 HOH D 19 1439 82 HOH HOH . V 4 HOH D 20 1440 83 HOH HOH . V 4 HOH D 21 1441 85 HOH HOH . V 4 HOH D 22 1442 90 HOH HOH . V 4 HOH D 23 1443 94 HOH HOH . V 4 HOH D 24 1444 97 HOH HOH . V 4 HOH D 25 1445 98 HOH HOH . V 4 HOH D 26 1446 102 HOH HOH . W 4 HOH E 1 1521 3 HOH HOH . W 4 HOH E 2 1522 8 HOH HOH . W 4 HOH E 3 1523 9 HOH HOH . W 4 HOH E 4 1524 15 HOH HOH . W 4 HOH E 5 1525 19 HOH HOH . W 4 HOH E 6 1526 20 HOH HOH . W 4 HOH E 7 1527 23 HOH HOH . W 4 HOH E 8 1528 26 HOH HOH . W 4 HOH E 9 1529 39 HOH HOH . W 4 HOH E 10 1530 40 HOH HOH . W 4 HOH E 11 1531 48 HOH HOH . W 4 HOH E 12 1532 49 HOH HOH . W 4 HOH E 13 1533 55 HOH HOH . W 4 HOH E 14 1534 61 HOH HOH . W 4 HOH E 15 1535 65 HOH HOH . W 4 HOH E 16 1536 68 HOH HOH . W 4 HOH E 17 1537 75 HOH HOH . W 4 HOH E 18 1538 84 HOH HOH . W 4 HOH E 19 1539 88 HOH HOH . W 4 HOH E 20 1540 93 HOH HOH . W 4 HOH E 21 1541 95 HOH HOH . W 4 HOH E 22 1542 96 HOH HOH . W 4 HOH E 23 1543 101 HOH HOH . W 4 HOH E 24 1544 103 HOH HOH . X 4 HOH F 1 1621 12 HOH HOH . X 4 HOH F 2 1622 14 HOH HOH . X 4 HOH F 3 1623 18 HOH HOH . X 4 HOH F 4 1624 24 HOH HOH . X 4 HOH F 5 1625 33 HOH HOH . X 4 HOH F 6 1626 41 HOH HOH . X 4 HOH F 7 1627 47 HOH HOH . X 4 HOH F 8 1628 56 HOH HOH . X 4 HOH F 9 1629 57 HOH HOH . X 4 HOH F 10 1630 64 HOH HOH . X 4 HOH F 11 1631 69 HOH HOH . X 4 HOH F 12 1632 73 HOH HOH . X 4 HOH F 13 1633 77 HOH HOH . X 4 HOH F 14 1634 86 HOH HOH . X 4 HOH F 15 1635 92 HOH HOH . X 4 HOH F 16 1636 104 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CHA HEM . . . R 3 -4.313 11.784 44.266 1 36.74 ? CHA HEM 1620 F 1 HETATM 2 C CHB HEM . . . R 3 -0.649 13.305 41.627 1 36.47 ? CHB HEM 1620 F 1 HETATM 3 C CHC HEM . . . R 3 1.7 14.666 45.595 1 35.72 ? CHC HEM 1620 F 1 HETATM 4 C CHD HEM . . . R 3 -1.992 13.096 48.278 1 37.42 ? CHD HEM 1620 F 1 HETATM 5 C C1A HEM . . . R 3 -3.538 12.05 43.183 1 37.87 ? C1A HEM 1620 F 1 HETATM 6 C C2A HEM . . . R 3 -3.92 11.807 41.807 1 38 ? C2A HEM 1620 F 1 HETATM 7 C C3A HEM . . . R 3 -2.885 12.23 41.04 1 38.21 ? C3A HEM 1620 F 1 HETATM 8 C C4A HEM . . . R 3 -1.844 12.752 41.955 1 37.84 ? C4A HEM 1620 F 1 HETATM 9 C CMA HEM . . . R 3 -2.768 12.192 39.491 1 40 ? CMA HEM 1620 F 1 HETATM 10 C CAA HEM . . . R 3 -5.281 11.174 41.398 1 38.17 ? CAA HEM 1620 F 1 HETATM 11 C CBA HEM . . . R 3 -5.321 9.968 40.479 1 36.88 ? CBA HEM 1620 F 1 HETATM 12 C CGA HEM . . . R 3 -6.772 9.57 40.236 1 36.42 ? CGA HEM 1620 F 1 HETATM 13 O O1A HEM . . . R 3 -7.344 10.174 39.217 1 34.01 ? O1A HEM 1620 F 1 HETATM 14 O O2A HEM . . . R 3 -7.297 8.728 40.999 1 35.87 ? O2A HEM 1620 F 1 HETATM 15 C C1B HEM . . . R 3 0.329 13.802 42.447 1 36.16 ? C1B HEM 1620 F 1 HETATM 16 C C2B HEM . . . R 3 1.595 14.375 41.99 1 35.34 ? C2B HEM 1620 F 1 HETATM 17 C C3B HEM . . . R 3 2.267 14.772 43.123 1 34.76 ? C3B HEM 1620 F 1 HETATM 18 C C4B HEM . . . R 3 1.426 14.435 44.244 1 35.31 ? C4B HEM 1620 F 1 HETATM 19 C CMB HEM . . . R 3 2.039 14.483 40.507 1 34.84 ? CMB HEM 1620 F 1 HETATM 20 C CAB HEM . . . R 3 3.663 15.442 43.278 1 35.13 ? CAB HEM 1620 F 1 HETATM 21 C CBB HEM . . . R 3 4.864 14.643 42.749 1 35.03 ? CBB HEM 1620 F 1 HETATM 22 C C1C HEM . . . R 3 0.903 14.344 46.685 1 35.64 ? C1C HEM 1620 F 1 HETATM 23 C C2C HEM . . . R 3 1.266 14.622 48.084 1 34.8 ? C2C HEM 1620 F 1 HETATM 24 C C3C HEM . . . R 3 0.224 14.18 48.847 1 33.81 ? C3C HEM 1620 F 1 HETATM 25 C C4C HEM . . . R 3 -0.756 13.641 47.929 1 35.84 ? C4C HEM 1620 F 1 HETATM 26 C CMC HEM . . . R 3 2.621 15.292 48.5 1 36.68 ? CMC HEM 1620 F 1 HETATM 27 C CAC HEM . . . R 3 0.003 14.182 50.39 1 33.05 ? CAC HEM 1620 F 1 HETATM 28 C CBC HEM . . . R 3 -0.1 15.544 51.058 1 32.57 ? CBC HEM 1620 F 1 HETATM 29 C C1D HEM . . . R 3 -2.965 12.579 47.437 1 37.39 ? C1D HEM 1620 F 1 HETATM 30 C C2D HEM . . . R 3 -4.267 12.023 47.837 1 36.85 ? C2D HEM 1620 F 1 HETATM 31 C C3D HEM . . . R 3 -4.92 11.665 46.677 1 37.09 ? C3D HEM 1620 F 1 HETATM 32 C C4D HEM . . . R 3 -4.017 11.986 45.585 1 37.12 ? C4D HEM 1620 F 1 HETATM 33 C CMD HEM . . . R 3 -4.767 11.886 49.292 1 33.84 ? CMD HEM 1620 F 1 HETATM 34 C CAD HEM . . . R 3 -6.339 11.054 46.496 1 36.58 ? CAD HEM 1620 F 1 HETATM 35 C CBD HEM . . . R 3 -6.581 9.603 47.011 1 33.77 ? CBD HEM 1620 F 1 HETATM 36 C CGD HEM . . . R 3 -8.022 9.193 46.761 1 34.15 ? CGD HEM 1620 F 1 HETATM 37 O O1D HEM . . . R 3 -8.973 10.001 46.977 1 30.31 ? O1D HEM 1620 F 1 HETATM 38 O O2D HEM . . . R 3 -8.159 8.032 46.328 1 35.11 ? O2D HEM 1620 F 1 HETATM 39 N NA HEM . . . R 3 -2.3 12.637 43.238 1 38.4 ? NA HEM 1620 F 1 HETATM 40 N NB HEM . . . R 3 0.247 13.862 43.821 1 36.89 ? NB HEM 1620 F 1 HETATM 41 N NC HEM . . . R 3 -0.336 13.767 46.615 1 36.58 ? NC HEM 1620 F 1 HETATM 42 N ND HEM . . . R 3 -2.841 12.559 46.034 1 37.43 ? ND HEM 1620 F 1 HETATM 43 FE FE HEM . . . R 3 -1.306 13.175 44.951 1 38.48 ? FE HEM 1620 F 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #