data_9GCX # _model_server_result.job_id fh8zggm8NtJr-oG3b5r-3Q _model_server_result.datetime_utc '2025-01-22 19:59:02' _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 9gcx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":501}' # _entry.id 9GCX # _exptl.entry_id 9GCX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 16 _entity.src_method nat _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 9GCX _cell.length_a 210.082 _cell.length_b 210.082 _cell.length_c 344.844 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9GCX _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 22-meric _pdbx_struct_assembly.oligomeric_count 22 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression 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 1 1 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 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' 10_445 -y-1,-x-1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -105.041 -181.936349 57.474 # _struct_asym.details ? _struct_asym.entity_id 16 _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 222 E CYS 144 1_555 E SG CYS 238 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf2 H SG CYS 55 H CYS 24 1_555 H SG CYS 99 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 H SG CYS 71 H CYS 40 1_555 H SG CYS 85 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? covale ? covale1 D SG CYS 121 D CYS 37 1_555 V CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.759 ? covale ? covale2 D SG CYS 124 D CYS 40 1_555 V CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 N FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 O FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 N FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 O FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc5 D NE2 HIS 125 D HIS 41 1_555 V FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc6 D SD MET 244 D MET 160 1_555 V FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc7 E SG CYS 217 E CYS 139 1_555 X FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc8 E ND1 HIS 219 E HIS 141 1_555 X FE2 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc9 E SG CYS 236 E CYS 158 1_555 X FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc10 E ND1 HIS 239 E HIS 161 1_555 X FE2 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _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 439 n n FE NB HEC sing 440 n n FE NC HEC sing 441 n n FE ND HEC sing 442 n n CHA C1A HEC doub 443 n n CHA C4D HEC sing 444 n n CHA HHA HEC sing 445 n n CHB C4A HEC doub 446 n n CHB C1B HEC sing 447 n n CHB HHB HEC sing 448 n n CHC C4B HEC doub 449 n n CHC C1C HEC sing 450 n n CHC HHC HEC sing 451 n n CHD C4C HEC doub 452 n n CHD C1D HEC sing 453 n n CHD HHD HEC sing 454 n n NA C1A HEC sing 455 n y NA C4A HEC sing 456 n y C1A C2A HEC sing 457 n y C2A C3A HEC doub 458 n y C2A CAA HEC sing 459 n n C3A C4A HEC sing 460 n y C3A CMA HEC sing 461 n n CMA HMA1 HEC sing 462 n n CMA HMA2 HEC sing 463 n n CMA HMA3 HEC sing 464 n n CAA CBA HEC sing 465 n n CAA HAA1 HEC sing 466 n n CAA HAA2 HEC sing 467 n n CBA CGA HEC sing 468 n n CBA HBA1 HEC sing 469 n n CBA HBA2 HEC sing 470 n n CGA O1A HEC doub 471 n n CGA O2A HEC sing 472 n n O2A H2A HEC sing 473 n n NB C1B HEC sing 474 n y NB C4B HEC sing 475 n y C1B C2B HEC doub 476 n y C2B C3B HEC sing 477 n y C2B CMB HEC sing 478 n n C3B C4B HEC sing 479 n y C3B CAB HEC doub 480 e n CMB HMB1 HEC sing 481 n n CMB HMB2 HEC sing 482 n n CMB HMB3 HEC sing 483 n n CAB CBB HEC sing 484 n n CAB HAB HEC sing 485 n n CBB HBB1 HEC sing 486 n n CBB HBB2 HEC sing 487 n n CBB HBB3 HEC sing 488 n n NC C1C HEC sing 489 n y NC C4C HEC sing 490 n y C1C C2C HEC doub 491 n y C2C C3C HEC sing 492 n y C2C CMC HEC sing 493 n n C3C C4C HEC sing 494 n y C3C CAC HEC doub 495 e n CMC HMC1 HEC sing 496 n n CMC HMC2 HEC sing 497 n n CMC HMC3 HEC sing 498 n n CAC CBC HEC sing 499 n n CAC HAC HEC sing 500 n n CBC HBC1 HEC sing 501 n n CBC HBC2 HEC sing 502 n n CBC HBC3 HEC sing 503 n n ND C1D HEC sing 504 n y ND C4D HEC sing 505 n y C1D C2D HEC doub 506 n y C2D C3D HEC sing 507 n y C2D CMD HEC sing 508 n n C3D C4D HEC doub 509 n y C3D CAD HEC sing 510 n n CMD HMD1 HEC sing 511 n n CMD HMD2 HEC sing 512 n n CMD HMD3 HEC sing 513 n n CAD CBD HEC sing 514 n n CAD HAD1 HEC sing 515 n n CAD HAD2 HEC sing 516 n n CBD CGD HEC sing 517 n n CBD HBD1 HEC sing 518 n n CBD HBD2 HEC sing 519 n n CGD O1D HEC doub 520 n n CGD O2D HEC sing 521 n n O2D H2D HEC sing 522 n n # _atom_sites.entry_id 9GCX _atom_sites.fract_transf_matrix[1][1] 0.00476 _atom_sites.fract_transf_matrix[1][2] 0.002748 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005496 _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] 0.0029 _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 L 11 LOP A 1 501 501 LOP LOP . M 12 CDL A 1 502 502 CDL CDL . N 13 HEM C 1 501 501 HEM HEM . O 13 HEM C 1 502 502 HEM HEM . P 11 LOP C 1 503 503 LOP LOP . Q 12 CDL C 1 504 504 CDL CDL . R 14 A1IKG C 1 505 509 A1IKG SG1 . S 11 LOP C 1 506 512 LOP LOP . T 11 LOP C 1 507 513 LOP LOP . U 15 LMT C 1 508 515 LMT LMT . V 16 HEC D 1 501 501 HEC HEC . W 12 CDL D 1 502 502 CDL CDL . X 17 FES E 1 201 201 FES FES . Y 11 LOP E 1 202 201 LOP LOP . Z 18 PSC E 1 203 202 PSC PSC . AA 19 SO4 F 1 201 3 SO4 SO4 . BA 11 LOP G 1 101 514 LOP LOP . CA 19 SO4 G 1 102 1 SO4 SO4 . DA 19 SO4 G 1 103 2 SO4 SO4 . EA 20 HOH A 1 601 301 HOH HOH . EA 20 HOH A 2 602 521 HOH HOH . EA 20 HOH A 3 603 518 HOH HOH . FA 20 HOH B 1 501 522 HOH HOH . GA 20 HOH C 1 601 16 HOH HOH . GA 20 HOH C 2 602 254 HOH HOH . GA 20 HOH C 3 603 523 HOH HOH . GA 20 HOH C 4 604 516 HOH HOH . HA 20 HOH E 1 301 514 HOH HOH . IA 20 HOH F 1 301 519 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 16 -17.699 -82.616 38.417 1 125.75 ? FE HEC 501 D 1 HETATM 2 C CHA HEC . . . V 16 -20.012 -82.625 40.94 1 140.53 ? CHA HEC 501 D 1 HETATM 3 C CHB HEC . . . V 16 -19.068 -79.772 37.091 1 127.1 ? CHB HEC 501 D 1 HETATM 4 C CHC HEC . . . V 16 -15.266 -82.489 35.882 1 140.1 ? CHC HEC 501 D 1 HETATM 5 C CHD HEC . . . V 16 -16.406 -85.54 39.611 1 135.74 ? CHD HEC 501 D 1 HETATM 6 N NA HEC . . . V 16 -19.28 -81.401 38.93 1 124.77 ? NA HEC 501 D 1 HETATM 7 C C1A HEC . . . V 16 -20.112 -81.536 39.96 1 133.61 ? C1A HEC 501 D 1 HETATM 8 C C2A HEC . . . V 16 -21.152 -80.481 40.079 1 138.85 ? C2A HEC 501 D 1 HETATM 9 C C3A HEC . . . V 16 -20.858 -79.639 38.909 1 139.23 ? C3A HEC 501 D 1 HETATM 10 C C4A HEC . . . V 16 -19.686 -80.301 38.305 1 128.86 ? C4A HEC 501 D 1 HETATM 11 C CMA HEC . . . V 16 -21.547 -78.388 38.436 1 149.81 ? CMA HEC 501 D 1 HETATM 12 C CAA HEC . . . V 16 -22.265 -80.354 41.111 1 132.07 ? CAA HEC 501 D 1 HETATM 13 C CBA HEC . . . V 16 -22.159 -79.181 42.083 1 128.52 ? CBA HEC 501 D 1 HETATM 14 C CGA HEC . . . V 16 -23.362 -79.305 42.991 1 137.58 ? CGA HEC 501 D 1 HETATM 15 O O1A HEC . . . V 16 -23.808 -80.444 43.194 1 141.53 ? O1A HEC 501 D 1 HETATM 16 O O2A HEC . . . V 16 -23.903 -78.299 43.499 1 150.54 ? O2A HEC 501 D 1 HETATM 17 N NB HEC . . . V 16 -17.258 -81.37 36.777 1 125.75 ? NB HEC 501 D 1 HETATM 18 C C1B HEC . . . V 16 -17.907 -80.272 36.381 1 125.09 ? C1B HEC 501 D 1 HETATM 19 C C2B HEC . . . V 16 -17.398 -79.561 35.19 1 121.85 ? C2B HEC 501 D 1 HETATM 20 C C3B HEC . . . V 16 -16.267 -80.389 34.857 1 125.3 ? C3B HEC 501 D 1 HETATM 21 C C4B HEC . . . V 16 -16.265 -81.442 35.878 1 127.37 ? C4B HEC 501 D 1 HETATM 22 C CMB HEC . . . V 16 -17.888 -78.316 34.522 1 116.41 ? CMB HEC 501 D 1 HETATM 23 C CAB HEC . . . V 16 -15.328 -80.169 33.698 1 131.92 ? CAB HEC 501 D 1 HETATM 24 C CBB HEC . . . V 16 -15.005 -78.694 33.55 1 136.22 ? CBB HEC 501 D 1 HETATM 25 N NC HEC . . . V 16 -16.109 -83.799 37.854 1 140.33 ? NC HEC 501 D 1 HETATM 26 C C1C HEC . . . V 16 -15.227 -83.62 36.819 1 150.95 ? C1C HEC 501 D 1 HETATM 27 C C2C HEC . . . V 16 -14.192 -84.68 36.659 1 150.33 ? C2C HEC 501 D 1 HETATM 28 C C3C HEC . . . V 16 -14.57 -85.518 37.814 1 146.79 ? C3C HEC 501 D 1 HETATM 29 C C4C HEC . . . V 16 -15.748 -84.93 38.452 1 141.72 ? C4C HEC 501 D 1 HETATM 30 C CMC HEC . . . V 16 -13.08 -84.805 35.64 1 146.46 ? CMC HEC 501 D 1 HETATM 31 C CAC HEC . . . V 16 -13.998 -86.824 38.241 1 140.99 ? CAC HEC 501 D 1 HETATM 32 C CBC HEC . . . V 16 -12.554 -86.622 38.709 1 135.47 ? CBC HEC 501 D 1 HETATM 33 N ND HEC . . . V 16 -18.123 -83.881 40.021 1 133.14 ? ND HEC 501 D 1 HETATM 34 C C1D HEC . . . V 16 -17.53 -85.023 40.382 1 137.51 ? C1D HEC 501 D 1 HETATM 35 C C2D HEC . . . V 16 -18.079 -85.71 41.6 1 147.67 ? C2D HEC 501 D 1 HETATM 36 C C3D HEC . . . V 16 -19.17 -84.808 41.993 1 145.52 ? C3D HEC 501 D 1 HETATM 37 C C4D HEC . . . V 16 -19.084 -83.75 40.951 1 142.22 ? C4D HEC 501 D 1 HETATM 38 C CMD HEC . . . V 16 -17.668 -86.998 42.288 1 147.54 ? CMD HEC 501 D 1 HETATM 39 C CAD HEC . . . V 16 -20.134 -84.919 43.157 1 141.16 ? CAD HEC 501 D 1 HETATM 40 C CBD HEC . . . V 16 -19.715 -83.905 44.223 1 141.13 ? CBD HEC 501 D 1 HETATM 41 C CGD HEC . . . V 16 -20.321 -84.134 45.598 1 148.21 ? CGD HEC 501 D 1 HETATM 42 O O1D HEC . . . V 16 -20.074 -83.301 46.496 1 140.8 ? O1D HEC 501 D 1 HETATM 43 O O2D HEC . . . V 16 -21.031 -85.136 45.831 1 162.56 ? O2D HEC 501 D 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #