data_3E5K # _model_server_result.job_id T_rBdPvs8VfSuk3W-Nx1hA _model_server_result.datetime_utc '2024-10-19 11:26:27' _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 3e5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1408}' # _entry.id 3E5K # _exptl.entry_id 3E5K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3E5K _cell.length_a 143.725 _cell.length_b 143.725 _cell.length_c 70.943 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E5K _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1 A,B,C,D 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -47.295333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A SG CYS 348 A CYS 348 1_555 B FE HEM . A HEM 1408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc2 C N3 PIM . A PIM 501 1_555 B FE HEM . A HEM 1408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? # _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 # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag CHA C1A HEM sing 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 3E5K _atom_sites.fract_transf_matrix[1][1] 0.006958 _atom_sites.fract_transf_matrix[1][2] 0.004017 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008034 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.014096 _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 B 2 HEM A 1 1408 1408 HEM HEM . C 3 PIM A 1 501 501 PIM PIM . D 4 HOH A 1 1409 1 HOH HOH . D 4 HOH A 2 1410 2 HOH HOH . D 4 HOH A 3 1411 3 HOH HOH . D 4 HOH A 4 1412 4 HOH HOH . D 4 HOH A 5 1413 5 HOH HOH . D 4 HOH A 6 1414 6 HOH HOH . D 4 HOH A 7 1415 7 HOH HOH . D 4 HOH A 8 1416 8 HOH HOH . D 4 HOH A 9 1417 9 HOH HOH . D 4 HOH A 10 1418 10 HOH HOH . D 4 HOH A 11 1419 11 HOH HOH . D 4 HOH A 12 1420 12 HOH HOH . D 4 HOH A 13 1421 13 HOH HOH . D 4 HOH A 14 1422 14 HOH HOH . D 4 HOH A 15 1423 15 HOH HOH . D 4 HOH A 16 1424 16 HOH HOH . D 4 HOH A 17 1425 17 HOH HOH . D 4 HOH A 18 1426 18 HOH HOH . D 4 HOH A 19 1427 19 HOH HOH . D 4 HOH A 20 1428 20 HOH HOH . D 4 HOH A 21 1429 21 HOH HOH . D 4 HOH A 22 1430 22 HOH HOH . D 4 HOH A 23 1431 23 HOH HOH . D 4 HOH A 24 1432 24 HOH HOH . D 4 HOH A 25 1433 25 HOH HOH . D 4 HOH A 26 1434 26 HOH HOH . D 4 HOH A 27 1435 27 HOH HOH . D 4 HOH A 28 1436 28 HOH HOH . D 4 HOH A 29 1437 29 HOH HOH . D 4 HOH A 30 1438 30 HOH HOH . D 4 HOH A 31 1439 31 HOH HOH . D 4 HOH A 32 1440 32 HOH HOH . D 4 HOH A 33 1441 33 HOH HOH . D 4 HOH A 34 1442 34 HOH HOH . D 4 HOH A 35 1443 35 HOH HOH . D 4 HOH A 36 1444 36 HOH HOH . D 4 HOH A 37 1445 37 HOH HOH . D 4 HOH A 38 1446 38 HOH HOH . D 4 HOH A 39 1447 39 HOH HOH . D 4 HOH A 40 1448 40 HOH HOH . D 4 HOH A 41 1449 41 HOH HOH . D 4 HOH A 42 1450 42 HOH HOH . D 4 HOH A 43 1451 43 HOH HOH . D 4 HOH A 44 1452 44 HOH HOH . D 4 HOH A 45 1453 45 HOH HOH . D 4 HOH A 46 1454 46 HOH HOH . D 4 HOH A 47 1455 47 HOH HOH . D 4 HOH A 48 1456 48 HOH HOH . D 4 HOH A 49 1457 49 HOH HOH . D 4 HOH A 50 1458 50 HOH HOH . D 4 HOH A 51 1459 51 HOH HOH . D 4 HOH A 52 1460 52 HOH HOH . D 4 HOH A 53 1461 53 HOH HOH . D 4 HOH A 54 1462 54 HOH HOH . D 4 HOH A 55 1463 55 HOH HOH . D 4 HOH A 56 1464 56 HOH HOH . D 4 HOH A 57 1465 57 HOH HOH . D 4 HOH A 58 1466 58 HOH HOH . D 4 HOH A 59 1467 59 HOH HOH . D 4 HOH A 60 1468 60 HOH HOH . D 4 HOH A 61 1469 61 HOH HOH . D 4 HOH A 62 1470 62 HOH HOH . D 4 HOH A 63 1471 63 HOH HOH . D 4 HOH A 64 1472 64 HOH HOH . D 4 HOH A 65 1473 65 HOH HOH . D 4 HOH A 66 1474 66 HOH HOH . D 4 HOH A 67 1475 67 HOH HOH . D 4 HOH A 68 1476 68 HOH HOH . D 4 HOH A 69 1477 69 HOH HOH . D 4 HOH A 70 1478 70 HOH HOH . D 4 HOH A 71 1479 71 HOH HOH . D 4 HOH A 72 1480 72 HOH HOH . D 4 HOH A 73 1481 73 HOH HOH . D 4 HOH A 74 1482 74 HOH HOH . D 4 HOH A 75 1483 75 HOH HOH . D 4 HOH A 76 1484 76 HOH HOH . D 4 HOH A 77 1485 77 HOH HOH . D 4 HOH A 78 1486 78 HOH HOH . D 4 HOH A 79 1487 79 HOH HOH . D 4 HOH A 80 1488 80 HOH HOH . D 4 HOH A 81 1489 81 HOH HOH . D 4 HOH A 82 1490 82 HOH HOH . D 4 HOH A 83 1491 83 HOH HOH . D 4 HOH A 84 1492 84 HOH HOH . D 4 HOH A 85 1493 85 HOH HOH . D 4 HOH A 86 1494 86 HOH HOH . D 4 HOH A 87 1495 87 HOH HOH . D 4 HOH A 88 1496 88 HOH HOH . D 4 HOH A 89 1497 89 HOH HOH . D 4 HOH A 90 1498 90 HOH HOH . D 4 HOH A 91 1499 91 HOH HOH . D 4 HOH A 92 1500 92 HOH HOH . D 4 HOH A 93 1501 93 HOH HOH . D 4 HOH A 94 1502 94 HOH HOH . D 4 HOH A 95 1503 95 HOH HOH . D 4 HOH A 96 1504 96 HOH HOH . D 4 HOH A 97 1505 97 HOH HOH . D 4 HOH A 98 1506 98 HOH HOH . D 4 HOH A 99 1507 99 HOH HOH . D 4 HOH A 100 1508 100 HOH HOH . D 4 HOH A 101 1509 101 HOH HOH . D 4 HOH A 102 1510 102 HOH HOH . D 4 HOH A 103 1511 103 HOH HOH . D 4 HOH A 104 1512 104 HOH HOH . D 4 HOH A 105 1513 105 HOH HOH . D 4 HOH A 106 1514 106 HOH HOH . D 4 HOH A 107 1515 107 HOH HOH . D 4 HOH A 108 1516 108 HOH HOH . D 4 HOH A 109 1517 109 HOH HOH . D 4 HOH A 110 1518 110 HOH HOH . D 4 HOH A 111 1519 111 HOH HOH . D 4 HOH A 112 1520 112 HOH HOH . D 4 HOH A 113 1521 113 HOH HOH . D 4 HOH A 114 1522 114 HOH HOH . D 4 HOH A 115 1523 115 HOH HOH . D 4 HOH A 116 1524 116 HOH HOH . D 4 HOH A 117 1525 117 HOH HOH . D 4 HOH A 118 1526 118 HOH HOH . D 4 HOH A 119 1527 119 HOH HOH . D 4 HOH A 120 1528 120 HOH HOH . D 4 HOH A 121 1529 121 HOH HOH . D 4 HOH A 122 1530 122 HOH HOH . D 4 HOH A 123 1531 123 HOH HOH . D 4 HOH A 124 1532 124 HOH HOH . D 4 HOH A 125 1533 125 HOH HOH . D 4 HOH A 126 1534 126 HOH HOH . D 4 HOH A 127 1535 127 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 . . . B 2 -55.323 54.086 -28.995 1 37.46 ? CHA HEM 1408 A 1 HETATM 2 C CHB HEM . . . B 2 -58.339 53.241 -25.429 1 40.08 ? CHB HEM 1408 A 1 HETATM 3 C CHC HEM . . . B 2 -55.643 49.681 -23.833 1 31.38 ? CHC HEM 1408 A 1 HETATM 4 C CHD HEM . . . B 2 -52.567 50.491 -27.523 1 29.87 ? CHD HEM 1408 A 1 HETATM 5 C C1A HEM . . . B 2 -56.348 54.088 -28.1 1 38.09 ? C1A HEM 1408 A 1 HETATM 6 C C2A HEM . . . B 2 -57.44 55.02 -28.275 1 35.85 ? C2A HEM 1408 A 1 HETATM 7 C C3A HEM . . . B 2 -58.235 54.815 -27.219 1 37.02 ? C3A HEM 1408 A 1 HETATM 8 C C4A HEM . . . B 2 -57.646 53.705 -26.515 1 37.89 ? C4A HEM 1408 A 1 HETATM 9 C CMA HEM . . . B 2 -59.6 55.427 -26.804 1 33.79 ? CMA HEM 1408 A 1 HETATM 10 C CAA HEM . . . B 2 -57.543 56.049 -29.417 1 32.19 ? CAA HEM 1408 A 1 HETATM 11 C CBA HEM . . . B 2 -57.198 57.466 -28.898 1 31.08 ? CBA HEM 1408 A 1 HETATM 12 C CGA HEM . . . B 2 -57.698 58.444 -29.956 1 46.63 ? CGA HEM 1408 A 1 HETATM 13 O O1A HEM . . . B 2 -58.38 58.105 -30.968 1 51.72 ? O1A HEM 1408 A 1 HETATM 14 O O2A HEM . . . B 2 -57.547 59.69 -29.95 1 53.88 ? O2A HEM 1408 A 1 HETATM 15 C C1B HEM . . . B 2 -57.919 52.21 -24.655 1 32 ? C1B HEM 1408 A 1 HETATM 16 C C2B HEM . . . B 2 -58.54 51.852 -23.413 1 37.16 ? C2B HEM 1408 A 1 HETATM 17 C C3B HEM . . . B 2 -57.732 50.867 -23.02 1 27.36 ? C3B HEM 1408 A 1 HETATM 18 C C4B HEM . . . B 2 -56.644 50.629 -23.91 1 28.59 ? C4B HEM 1408 A 1 HETATM 19 C CMB HEM . . . B 2 -59.824 52.387 -22.702 1 27.68 ? CMB HEM 1408 A 1 HETATM 20 C CAB HEM . . . B 2 -58.132 50.085 -21.774 1 29.25 ? CAB HEM 1408 A 1 HETATM 21 C CBB HEM . . . B 2 -57.138 49.245 -21.68 1 30.76 ? CBB HEM 1408 A 1 HETATM 22 C C1C HEM . . . B 2 -54.646 49.571 -24.776 1 32.87 ? C1C HEM 1408 A 1 HETATM 23 C C2C HEM . . . B 2 -53.671 48.487 -24.802 1 30.14 ? C2C HEM 1408 A 1 HETATM 24 C C3C HEM . . . B 2 -52.874 48.748 -25.845 1 33.99 ? C3C HEM 1408 A 1 HETATM 25 C C4C HEM . . . B 2 -53.293 49.981 -26.484 1 36.24 ? C4C HEM 1408 A 1 HETATM 26 C CMC HEM . . . B 2 -53.506 47.249 -23.9 1 24.27 ? CMC HEM 1408 A 1 HETATM 27 C CAC HEM . . . B 2 -51.626 47.987 -26.29 1 37.81 ? CAC HEM 1408 A 1 HETATM 28 C CBC HEM . . . B 2 -50.963 47.172 -25.441 1 43.72 ? CBC HEM 1408 A 1 HETATM 29 C C1D HEM . . . B 2 -52.95 51.63 -28.199 1 37.49 ? C1D HEM 1408 A 1 HETATM 30 C C2D HEM . . . B 2 -52.182 52.287 -29.242 1 35.6 ? C2D HEM 1408 A 1 HETATM 31 C C3D HEM . . . B 2 -53.069 53.417 -29.752 1 40.55 ? C3D HEM 1408 A 1 HETATM 32 C C4D HEM . . . B 2 -54.245 53.257 -28.916 1 37.48 ? C4D HEM 1408 A 1 HETATM 33 C CMD HEM . . . B 2 -50.813 51.857 -29.782 1 34.99 ? CMD HEM 1408 A 1 HETATM 34 C CAD HEM . . . B 2 -52.848 54.442 -30.891 1 37.42 ? CAD HEM 1408 A 1 HETATM 35 C CBD HEM . . . B 2 -53.229 53.626 -32.146 1 36.64 ? CBD HEM 1408 A 1 HETATM 36 C CGD HEM . . . B 2 -53.265 54.565 -33.342 1 43.35 ? CGD HEM 1408 A 1 HETATM 37 O O1D HEM . . . B 2 -53.435 54.032 -34.474 1 45.58 ? O1D HEM 1408 A 1 HETATM 38 O O2D HEM . . . B 2 -53.165 55.822 -33.14 1 38.66 ? O2D HEM 1408 A 1 HETATM 39 N NA HEM . . . B 2 -56.44 53.274 -27.003 1 33.73 ? NA HEM 1408 A 1 HETATM 40 N NB HEM . . . B 2 -56.791 51.533 -24.942 1 33.4 ? NB HEM 1408 A 1 HETATM 41 N NC HEM . . . B 2 -54.433 50.441 -25.849 1 29.41 ? NC HEM 1408 A 1 HETATM 42 N ND HEM . . . B 2 -54.152 52.271 -27.984 1 37.81 ? ND HEM 1408 A 1 HETATM 43 FE FE HEM . . . B 2 -55.399 51.87 -26.463 1 34.47 ? FE HEM 1408 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #