data_5OKD # _model_server_result.job_id C0K0WbsP8_CAhRgPBombIQ _model_server_result.datetime_utc '2024-11-23 10:54:05' _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 5okd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":501}' # _entry.id 5OKD # _exptl.entry_id 5OKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 18 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 5OKD _cell.length_a 209.871 _cell.length_b 209.871 _cell.length_c 342.097 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 18 _struct_asym.id V _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 disulf ? disulf1 E SG CYS 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 H SG CYS 37 H CYS 24 1_555 H SG CYS 81 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf3 H SG CYS 53 H CYS 40 1_555 H SG CYS 67 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 N FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 O FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 N FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 O FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc5 D NE2 HIS 125 D HIS 41 1_555 V FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc6 D SD MET 244 D MET 160 1_555 V FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 FE NA HEC sing 498 n n FE NB HEC sing 499 n n FE NC HEC sing 500 n n FE ND HEC sing 501 n n CHA C1A HEC doub 502 n n CHA C4D HEC sing 503 n n CHA HHA HEC sing 504 n n CHB C4A HEC doub 505 n n CHB C1B HEC sing 506 n n CHB HHB HEC sing 507 n n CHC C4B HEC doub 508 n n CHC C1C HEC sing 509 n n CHC HHC HEC sing 510 n n CHD C4C HEC doub 511 n n CHD C1D HEC sing 512 n n CHD HHD HEC sing 513 n n NA C1A HEC sing 514 n y NA C4A HEC sing 515 n y C1A C2A HEC sing 516 n y C2A C3A HEC doub 517 n y C2A CAA HEC sing 518 n n C3A C4A HEC sing 519 n y C3A CMA HEC sing 520 n n CMA HMA1 HEC sing 521 n n CMA HMA2 HEC sing 522 n n CMA HMA3 HEC sing 523 n n CAA CBA HEC sing 524 n n CAA HAA1 HEC sing 525 n n CAA HAA2 HEC sing 526 n n CBA CGA HEC sing 527 n n CBA HBA1 HEC sing 528 n n CBA HBA2 HEC sing 529 n n CGA O1A HEC doub 530 n n CGA O2A HEC sing 531 n n O2A H2A HEC sing 532 n n NB C1B HEC sing 533 n y NB C4B HEC sing 534 n y C1B C2B HEC doub 535 n y C2B C3B HEC sing 536 n y C2B CMB HEC sing 537 n n C3B C4B HEC sing 538 n y C3B CAB HEC doub 539 e n CMB HMB1 HEC sing 540 n n CMB HMB2 HEC sing 541 n n CMB HMB3 HEC sing 542 n n CAB CBB HEC sing 543 n n CAB HAB HEC sing 544 n n CBB HBB1 HEC sing 545 n n CBB HBB2 HEC sing 546 n n CBB HBB3 HEC sing 547 n n NC C1C HEC sing 548 n y NC C4C HEC sing 549 n y C1C C2C HEC doub 550 n y C2C C3C HEC sing 551 n y C2C CMC HEC sing 552 n n C3C C4C HEC sing 553 n y C3C CAC HEC doub 554 e n CMC HMC1 HEC sing 555 n n CMC HMC2 HEC sing 556 n n CMC HMC3 HEC sing 557 n n CAC CBC HEC sing 558 n n CAC HAC HEC sing 559 n n CBC HBC1 HEC sing 560 n n CBC HBC2 HEC sing 561 n n CBC HBC3 HEC sing 562 n n ND C1D HEC sing 563 n y ND C4D HEC sing 564 n y C1D C2D HEC doub 565 n y C2D C3D HEC sing 566 n y C2D CMD HEC sing 567 n n C3D C4D HEC doub 568 n y C3D CAD HEC sing 569 n n CMD HMD1 HEC sing 570 n n CMD HMD2 HEC sing 571 n n CMD HMD3 HEC sing 572 n n CAD CBD HEC sing 573 n n CAD HAD1 HEC sing 574 n n CAD HAD2 HEC sing 575 n n CBD CGD HEC sing 576 n n CBD HBD1 HEC sing 577 n n CBD HBD2 HEC sing 578 n n CGD O1D HEC doub 579 n n CGD O2D HEC sing 580 n n O2D H2D HEC sing 581 n n # _atom_sites.entry_id 5OKD _atom_sites.fract_transf_matrix[1][1] 0.004765 _atom_sites.fract_transf_matrix[1][2] 0.002751 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005502 _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] 0.002923 _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 K 11 PG4 A 1 501 503 PG4 PG4 . L 12 6PE A 1 502 1 6PE 6PE . M 13 CDL C 1 401 502 CDL CDL . N 14 HEM C 1 402 501 HEM HEM . O 14 HEM C 1 403 502 HEM HEM . P 15 9XE C 1 404 503 9XE SCK . Q 16 LMT C 1 405 506 LMT LMT . R 11 PG4 C 1 406 507 PG4 PG4 . S 11 PG4 C 1 407 508 PG4 PG4 . T 13 CDL C 1 408 501 CDL CDL . U 17 PEE C 1 409 1 PEE PEE . V 18 HEC D 1 501 501 HEC HEC . W 19 PO4 D 1 502 503 PO4 PO4 . X 13 CDL D 1 503 504 CDL CDL . Y 20 FES E 1 201 200 FES FES . Z 21 PX4 E 1 202 202 PX4 PX4 . AA 19 PO4 E 1 203 504 PO4 PO4 . BA 17 PEE E 1 204 2 PEE PEE . CA 13 CDL E 1 205 1 CDL CDL . DA 19 PO4 F 1 501 501 PO4 PO4 . EA 19 PO4 G 1 101 502 PO4 PO4 . FA 19 PO4 G 1 102 503 PO4 PO4 . GA 19 PO4 G 1 103 1 PO4 PO4 . HA 22 HOH A 1 601 111 HOH HOH . HA 22 HOH A 2 602 44 HOH HOH . HA 22 HOH A 3 603 51 HOH HOH . HA 22 HOH A 4 604 46 HOH HOH . HA 22 HOH A 5 605 64 HOH HOH . HA 22 HOH A 6 606 63 HOH HOH . HA 22 HOH A 7 607 54 HOH HOH . HA 22 HOH A 8 608 53 HOH HOH . HA 22 HOH A 9 609 36 HOH HOH . HA 22 HOH A 10 610 8 HOH HOH . HA 22 HOH A 11 611 17 HOH HOH . HA 22 HOH A 12 612 92 HOH HOH . HA 22 HOH A 13 613 56 HOH HOH . HA 22 HOH A 14 614 82 HOH HOH . HA 22 HOH A 15 615 87 HOH HOH . IA 22 HOH B 1 501 57 HOH HOH . IA 22 HOH B 2 502 5 HOH HOH . IA 22 HOH B 3 503 25 HOH HOH . IA 22 HOH B 4 504 27 HOH HOH . IA 22 HOH B 5 505 26 HOH HOH . IA 22 HOH B 6 506 91 HOH HOH . IA 22 HOH B 7 507 105 HOH HOH . IA 22 HOH B 8 508 30 HOH HOH . IA 22 HOH B 9 509 94 HOH HOH . IA 22 HOH B 10 510 47 HOH HOH . IA 22 HOH B 11 511 110 HOH HOH . IA 22 HOH B 12 512 100 HOH HOH . JA 22 HOH C 1 501 11 HOH HOH . JA 22 HOH C 2 502 10 HOH HOH . JA 22 HOH C 3 503 43 HOH HOH . JA 22 HOH C 4 504 55 HOH HOH . JA 22 HOH C 5 505 12 HOH HOH . JA 22 HOH C 6 506 41 HOH HOH . JA 22 HOH C 7 507 22 HOH HOH . JA 22 HOH C 8 508 67 HOH HOH . JA 22 HOH C 9 509 23 HOH HOH . JA 22 HOH C 10 510 33 HOH HOH . JA 22 HOH C 11 511 108 HOH HOH . JA 22 HOH C 12 512 31 HOH HOH . JA 22 HOH C 13 513 37 HOH HOH . JA 22 HOH C 14 514 101 HOH HOH . JA 22 HOH C 15 515 83 HOH HOH . JA 22 HOH C 16 516 104 HOH HOH . JA 22 HOH C 17 517 72 HOH HOH . JA 22 HOH C 18 518 71 HOH HOH . JA 22 HOH C 19 519 70 HOH HOH . JA 22 HOH C 20 520 95 HOH HOH . JA 22 HOH C 21 521 81 HOH HOH . JA 22 HOH C 22 522 103 HOH HOH . JA 22 HOH C 23 523 77 HOH HOH . JA 22 HOH C 24 524 79 HOH HOH . JA 22 HOH C 25 525 84 HOH HOH . JA 22 HOH C 26 526 106 HOH HOH . JA 22 HOH C 27 527 109 HOH HOH . KA 22 HOH D 1 601 49 HOH HOH . KA 22 HOH D 2 602 86 HOH HOH . KA 22 HOH D 3 603 90 HOH HOH . KA 22 HOH D 4 604 48 HOH HOH . KA 22 HOH D 5 605 96 HOH HOH . LA 22 HOH E 1 301 85 HOH HOH . LA 22 HOH E 2 302 99 HOH HOH . LA 22 HOH E 3 303 59 HOH HOH . LA 22 HOH E 4 304 9 HOH HOH . LA 22 HOH E 5 305 60 HOH HOH . LA 22 HOH E 6 306 21 HOH HOH . MA 22 HOH F 1 601 39 HOH HOH . MA 22 HOH F 2 602 58 HOH HOH . MA 22 HOH F 3 603 66 HOH HOH . MA 22 HOH F 4 604 88 HOH HOH . MA 22 HOH F 5 605 45 HOH HOH . MA 22 HOH F 6 606 28 HOH HOH . MA 22 HOH F 7 607 107 HOH HOH . MA 22 HOH F 8 608 73 HOH HOH . NA 22 HOH G 1 201 40 HOH HOH . NA 22 HOH G 2 202 50 HOH HOH . NA 22 HOH G 3 203 98 HOH HOH . NA 22 HOH G 4 204 52 HOH HOH . NA 22 HOH G 5 205 102 HOH HOH . OA 22 HOH H 1 101 65 HOH HOH . PA 22 HOH J 1 101 24 HOH HOH . PA 22 HOH J 2 102 18 HOH HOH . PA 22 HOH J 3 103 89 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 FE FE HEC . . . V 18 -17.654 -82.554 38.435 1 115.4 ? FE HEC 501 D 1 HETATM 2 C CHA HEC . . . V 18 -20.092 -82.666 40.908 1 114.55 ? CHA HEC 501 D 1 HETATM 3 C CHB HEC . . . V 18 -19.185 -79.762 37.031 1 111.83 ? CHB HEC 501 D 1 HETATM 4 C CHC HEC . . . V 18 -15.047 -82.252 36.183 1 116.94 ? CHC HEC 501 D 1 HETATM 5 C CHD HEC . . . V 18 -16.258 -85.483 39.694 1 118.12 ? CHD HEC 501 D 1 HETATM 6 N NA HEC . . . V 18 -19.358 -81.417 38.882 1 113.14 ? NA HEC 501 D 1 HETATM 7 C C1A HEC . . . V 18 -20.214 -81.581 39.914 1 113.68 ? C1A HEC 501 D 1 HETATM 8 C C2A HEC . . . V 18 -21.329 -80.594 39.981 1 112.44 ? C2A HEC 501 D 1 HETATM 9 C C3A HEC . . . V 18 -21.056 -79.736 38.816 1 112.21 ? C3A HEC 501 D 1 HETATM 10 C C4A HEC . . . V 18 -19.824 -80.338 38.23 1 112.46 ? C4A HEC 501 D 1 HETATM 11 C CMA HEC . . . V 18 -21.838 -78.54 38.338 1 111.49 ? CMA HEC 501 D 1 HETATM 12 C CAA HEC . . . V 18 -22.474 -80.489 40.965 1 111.97 ? CAA HEC 501 D 1 HETATM 13 C CBA HEC . . . V 18 -22.191 -79.501 42.091 1 113.75 ? CBA HEC 501 D 1 HETATM 14 C CGA HEC . . . V 18 -23.438 -79.366 42.941 1 113.99 ? CGA HEC 501 D 1 HETATM 15 O O1A HEC . . . V 18 -23.898 -80.381 43.506 1 114.68 ? O1A HEC 501 D 1 HETATM 16 O O2A HEC . . . V 18 -23.993 -78.252 43.053 1 113.82 ? O2A HEC 501 D 1 HETATM 17 N NB HEC . . . V 18 -17.2 -81.235 36.849 1 113.91 ? NB HEC 501 D 1 HETATM 18 C C1B HEC . . . V 18 -17.908 -80.17 36.418 1 112.51 ? C1B HEC 501 D 1 HETATM 19 C C2B HEC . . . V 18 -17.309 -79.399 35.292 1 112.62 ? C2B HEC 501 D 1 HETATM 20 C C3B HEC . . . V 18 -16.069 -80.151 35.066 1 114.07 ? C3B HEC 501 D 1 HETATM 21 C C4B HEC . . . V 18 -16.11 -81.243 36.068 1 114.78 ? C4B HEC 501 D 1 HETATM 22 C CMB HEC . . . V 18 -17.845 -78.175 34.593 1 112.21 ? CMB HEC 501 D 1 HETATM 23 C CAB HEC . . . V 18 -14.981 -79.92 34.061 1 114.85 ? CAB HEC 501 D 1 HETATM 24 C CBB HEC . . . V 18 -14.969 -78.796 33.05 1 114.18 ? CBB HEC 501 D 1 HETATM 25 N NC HEC . . . V 18 -15.949 -83.694 37.993 1 116.59 ? NC HEC 501 D 1 HETATM 26 C C1C HEC . . . V 18 -14.998 -83.416 37.085 1 117.96 ? C1C HEC 501 D 1 HETATM 27 C C2C HEC . . . V 18 -13.867 -84.384 37.006 1 120.39 ? C2C HEC 501 D 1 HETATM 28 C C3C HEC . . . V 18 -14.238 -85.351 38.059 1 120.62 ? C3C HEC 501 D 1 HETATM 29 C C4C HEC . . . V 18 -15.527 -84.827 38.592 1 118.36 ? C4C HEC 501 D 1 HETATM 30 C CMC HEC . . . V 18 -12.681 -84.324 36.073 1 121.58 ? CMC HEC 501 D 1 HETATM 31 C CAC HEC . . . V 18 -13.532 -86.591 38.516 1 121.98 ? CAC HEC 501 D 1 HETATM 32 C CBC HEC . . . V 18 -12.218 -87.107 37.965 1 123.81 ? CBC HEC 501 D 1 HETATM 33 N ND HEC . . . V 18 -18.108 -83.86 40.015 1 115.49 ? ND HEC 501 D 1 HETATM 34 C C1D HEC . . . V 18 -17.455 -84.976 40.386 1 117 ? C1D HEC 501 D 1 HETATM 35 C C2D HEC . . . V 18 -18.012 -85.67 41.581 1 117.44 ? C2D HEC 501 D 1 HETATM 36 C C3D HEC . . . V 18 -19.158 -84.829 41.938 1 115.94 ? C3D HEC 501 D 1 HETATM 37 C C4D HEC . . . V 18 -19.096 -83.748 40.923 1 115.08 ? C4D HEC 501 D 1 HETATM 38 C CMD HEC . . . V 18 -17.561 -86.938 42.262 1 118.57 ? CMD HEC 501 D 1 HETATM 39 C CAD HEC . . . V 18 -20.122 -85.022 43.083 1 115.7 ? CAD HEC 501 D 1 HETATM 40 C CBD HEC . . . V 18 -19.636 -84.132 44.228 1 116.8 ? CBD HEC 501 D 1 HETATM 41 C CGD HEC . . . V 18 -20.496 -84.244 45.469 1 117.01 ? CGD HEC 501 D 1 HETATM 42 O O1D HEC . . . V 18 -19.932 -84.11 46.58 1 117.39 ? O1D HEC 501 D 1 HETATM 43 O O2D HEC . . . V 18 -21.728 -84.452 45.353 1 115.89 ? O2D HEC 501 D 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #