data_4PV1 # _model_server_result.job_id QtRptIyhmqZJWmIHaye8jg _model_server_result.datetime_utc '2024-11-06 02:49:17' _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 4pv1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":304}' # _entry.id 4PV1 # _exptl.entry_id 4PV1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _entity.pdbx_number_of_molecules 4 _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 4PV1 _cell.length_a 159.085 _cell.length_b 159.085 _cell.length_c 361.322 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PV1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -79.5425 137.771651 60.220333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 11 K N N ? 11 L N N ? 11 M N N ? 11 W 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 disulf ? disulf1 D SG CYS 113 D CYS 113 1_555 D SG CYS 128 D CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 C SG CYS 25 C CYS 25 1_555 W CAC HEC . C HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc1 A NE2 HIS 86 A HIS 86 1_555 K FE HEC . A HEC 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc2 A NE2 HIS 100 A HIS 100 1_555 L FE HEC . A HEC 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 A NE2 HIS 187 A HIS 187 1_555 K FE HEC . A HEC 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc4 A NE2 HIS 202 A HIS 202 1_555 L FE HEC . A HEC 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc5 M FE HEC . A HEC 305 1_555 P O8 SMA . A SMA 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc6 M FE HEC . A HEC 305 1_555 CA O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc7 U MG CLA . B CLA 204 1_555 DA O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc8 C N TYR 1 C TYR 1 1_555 W FE HEC . C HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc9 C NE2 HIS 26 C HIS 26 1_555 W FE HEC . C HEC 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc10 D SG CYS 108 D CYS 108 1_555 X FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc11 D ND1 HIS 110 D HIS 110 1_555 X FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc12 D SG CYS 126 D CYS 126 1_555 X FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc13 D ND1 HIS 129 D HIS 129 1_555 X FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? # _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 524 n n FE NB HEC sing 525 n n FE NC HEC sing 526 n n FE ND HEC sing 527 n n CHA C1A HEC doub 528 n n CHA C4D HEC sing 529 n n CHA HHA HEC sing 530 n n CHB C4A HEC doub 531 n n CHB C1B HEC sing 532 n n CHB HHB HEC sing 533 n n CHC C4B HEC doub 534 n n CHC C1C HEC sing 535 n n CHC HHC HEC sing 536 n n CHD C4C HEC doub 537 n n CHD C1D HEC sing 538 n n CHD HHD HEC sing 539 n n NA C1A HEC sing 540 n y NA C4A HEC sing 541 n y C1A C2A HEC sing 542 n y C2A C3A HEC doub 543 n y C2A CAA HEC sing 544 n n C3A C4A HEC sing 545 n y C3A CMA HEC sing 546 n n CMA HMA1 HEC sing 547 n n CMA HMA2 HEC sing 548 n n CMA HMA3 HEC sing 549 n n CAA CBA HEC sing 550 n n CAA HAA1 HEC sing 551 n n CAA HAA2 HEC sing 552 n n CBA CGA HEC sing 553 n n CBA HBA1 HEC sing 554 n n CBA HBA2 HEC sing 555 n n CGA O1A HEC doub 556 n n CGA O2A HEC sing 557 n n O2A H2A HEC sing 558 n n NB C1B HEC sing 559 n y NB C4B HEC sing 560 n y C1B C2B HEC doub 561 n y C2B C3B HEC sing 562 n y C2B CMB HEC sing 563 n n C3B C4B HEC sing 564 n y C3B CAB HEC doub 565 e n CMB HMB1 HEC sing 566 n n CMB HMB2 HEC sing 567 n n CMB HMB3 HEC sing 568 n n CAB CBB HEC sing 569 n n CAB HAB HEC sing 570 n n CBB HBB1 HEC sing 571 n n CBB HBB2 HEC sing 572 n n CBB HBB3 HEC sing 573 n n NC C1C HEC sing 574 n y NC C4C HEC sing 575 n y C1C C2C HEC doub 576 n y C2C C3C HEC sing 577 n y C2C CMC HEC sing 578 n n C3C C4C HEC sing 579 n y C3C CAC HEC doub 580 e n CMC HMC1 HEC sing 581 n n CMC HMC2 HEC sing 582 n n CMC HMC3 HEC sing 583 n n CAC CBC HEC sing 584 n n CAC HAC HEC sing 585 n n CBC HBC1 HEC sing 586 n n CBC HBC2 HEC sing 587 n n CBC HBC3 HEC sing 588 n n ND C1D HEC sing 589 n y ND C4D HEC sing 590 n y C1D C2D HEC doub 591 n y C2D C3D HEC sing 592 n y C2D CMD HEC sing 593 n n C3D C4D HEC doub 594 n y C3D CAD HEC sing 595 n n CMD HMD1 HEC sing 596 n n CMD HMD2 HEC sing 597 n n CMD HMD3 HEC sing 598 n n CAD CBD HEC sing 599 n n CAD HAD1 HEC sing 600 n n CAD HAD2 HEC sing 601 n n CBD CGD HEC sing 602 n n CBD HBD1 HEC sing 603 n n CBD HBD2 HEC sing 604 n n CGD O1D HEC doub 605 n n CGD O2D HEC sing 606 n n O2D H2D HEC sing 607 n n # _atom_sites.entry_id 4PV1 _atom_sites.fract_transf_matrix[1][1] 0.006286 _atom_sites.fract_transf_matrix[1][2] 0.003629 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007258 _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] 0.002768 _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 I 9 MYS A 1 301 301 MYS MYS . J 10 CD A 1 302 302 CD CD . K 11 HEC A 1 303 303 HEC HEM . L 11 HEC A 1 304 304 HEC HEM . M 11 HEC A 1 305 305 HEC HEM . N 12 UMQ A 1 306 306 UMQ UMQ . O 12 UMQ A 1 307 307 UMQ UMQ . P 13 SMA A 1 308 308 SMA SMA . Q 14 7PH A 1 309 309 7PH 7PH . R 15 8K6 B 1 201 201 8K6 8K6 . S 10 CD B 1 202 202 CD CD . T 12 UMQ B 1 203 203 UMQ UMQ . U 16 CLA B 1 204 204 CLA CLA . V 17 OPC B 1 205 205 OPC OPC . W 11 HEC C 1 301 301 HEC HEM . X 18 FES D 1 201 201 FES FES . Y 19 SQD D 1 202 202 SQD SQD . Z 17 OPC D 1 203 203 OPC OPC . AA 17 OPC E 1 101 101 OPC OPC . BA 20 BCR G 1 101 101 BCR BCR . CA 21 HOH A 1 401 401 HOH HOH . CA 21 HOH A 2 402 402 HOH HOH . CA 21 HOH A 3 403 403 HOH HOH . CA 21 HOH A 4 404 404 HOH HOH . CA 21 HOH A 5 405 405 HOH HOH . CA 21 HOH A 6 406 406 HOH HOH . CA 21 HOH A 7 407 407 HOH HOH . CA 21 HOH A 8 408 408 HOH HOH . DA 21 HOH B 1 301 301 HOH HOH . DA 21 HOH B 2 302 302 HOH HOH . DA 21 HOH B 3 303 303 HOH HOH . DA 21 HOH B 4 304 304 HOH HOH . DA 21 HOH B 5 305 305 HOH HOH . EA 21 HOH C 1 1101 1101 HOH HOH . EA 21 HOH C 2 1102 1102 HOH HOH . FA 21 HOH G 1 201 201 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 . . . L 11 -28.113 71.047 13.151 1 62.24 ? FE HEC 304 A 1 HETATM 2 C CHA HEC . . . L 11 -25.881 73.561 12.588 1 68.49 ? CHA HEC 304 A 1 HETATM 3 C CHB HEC . . . L 11 -30.277 73.316 14.639 1 57.82 ? CHB HEC 304 A 1 HETATM 4 C CHC HEC . . . L 11 -30.586 68.659 13.343 1 66.72 ? CHC HEC 304 A 1 HETATM 5 C CHD HEC . . . L 11 -25.913 68.692 12.076 1 72.5 ? CHD HEC 304 A 1 HETATM 6 N NA HEC . . . L 11 -28.061 73.067 13.596 1 46.92 ? NA HEC 304 A 1 HETATM 7 C C1A HEC . . . L 11 -27.081 73.938 13.156 1 64.92 ? C1A HEC 304 A 1 HETATM 8 C C2A HEC . . . L 11 -27.543 75.292 13.41 1 74.34 ? C2A HEC 304 A 1 HETATM 9 C C3A HEC . . . L 11 -28.753 75.213 13.975 1 74.22 ? C3A HEC 304 A 1 HETATM 10 C C4A HEC . . . L 11 -29.107 73.814 14.106 1 63.45 ? C4A HEC 304 A 1 HETATM 11 C CMA HEC . . . L 11 -29.629 76.406 14.415 1 71.92 ? CMA HEC 304 A 1 HETATM 12 C CAA HEC . . . L 11 -26.793 76.608 13.089 1 74.15 ? CAA HEC 304 A 1 HETATM 13 C CBA HEC . . . L 11 -26.421 76.714 11.611 1 80.09 ? CBA HEC 304 A 1 HETATM 14 C CGA HEC . . . L 11 -27.609 76.439 10.723 1 81.34 ? CGA HEC 304 A 1 HETATM 15 O O1A HEC . . . L 11 -27.403 75.921 9.594 1 69.74 ? O1A HEC 304 A 1 HETATM 16 O O2A HEC . . . L 11 -28.76 76.735 11.135 1 91.76 ? O2A HEC 304 A 1 HETATM 17 N NB HEC . . . L 11 -30.079 71.006 13.842 1 61.05 ? NB HEC 304 A 1 HETATM 18 C C1B HEC . . . L 11 -30.759 72.037 14.461 1 66.13 ? C1B HEC 304 A 1 HETATM 19 C C2B HEC . . . L 11 -32.055 71.54 14.887 1 62.92 ? C2B HEC 304 A 1 HETATM 20 C C3B HEC . . . L 11 -32.141 70.247 14.521 1 50.18 ? C3B HEC 304 A 1 HETATM 21 C C4B HEC . . . L 11 -30.897 69.895 13.864 1 65.54 ? C4B HEC 304 A 1 HETATM 22 C CMB HEC . . . L 11 -33.105 72.409 15.618 1 65.7 ? CMB HEC 304 A 1 HETATM 23 C CAB HEC . . . L 11 -33.288 69.223 14.724 1 76.14 ? CAB HEC 304 A 1 HETATM 24 C CBB HEC . . . L 11 -34.389 69.444 15.451 1 76.59 ? CBB HEC 304 A 1 HETATM 25 N NC HEC . . . L 11 -28.201 69.009 12.886 1 67.08 ? NC HEC 304 A 1 HETATM 26 C C1C HEC . . . L 11 -29.377 68.293 12.795 1 68.82 ? C1C HEC 304 A 1 HETATM 27 C C2C HEC . . . L 11 -29.121 67.09 12.029 1 68.41 ? C2C HEC 304 A 1 HETATM 28 C C3C HEC . . . L 11 -27.823 67.097 11.668 1 59.44 ? C3C HEC 304 A 1 HETATM 29 C C4C HEC . . . L 11 -27.228 68.305 12.209 1 65.91 ? C4C HEC 304 A 1 HETATM 30 C CMC HEC . . . L 11 -30.213 66.042 11.718 1 66.26 ? CMC HEC 304 A 1 HETATM 31 C CAC HEC . . . L 11 -27.011 66.058 10.851 1 59.38 ? CAC HEC 304 A 1 HETATM 32 C CBC HEC . . . L 11 -27.473 64.86 10.474 1 72.82 ? CBC HEC 304 A 1 HETATM 33 N ND HEC . . . L 11 -26.206 71.123 12.355 1 61.26 ? ND HEC 304 A 1 HETATM 34 C C1D HEC . . . L 11 -25.432 69.979 12.182 1 68.37 ? C1D HEC 304 A 1 HETATM 35 C C2D HEC . . . L 11 -24.038 70.364 12.128 1 66.74 ? C2D HEC 304 A 1 HETATM 36 C C3D HEC . . . L 11 -24.034 71.89 12.293 1 61.33 ? C3D HEC 304 A 1 HETATM 37 C C4D HEC . . . L 11 -25.421 72.271 12.423 1 71.55 ? C4D HEC 304 A 1 HETATM 38 C CMD HEC . . . L 11 -22.814 69.441 11.951 1 72.34 ? CMD HEC 304 A 1 HETATM 39 C CAD HEC . . . L 11 -22.812 72.83 12.302 1 70.99 ? CAD HEC 304 A 1 HETATM 40 C CBD HEC . . . L 11 -22.3 72.958 10.872 1 70.49 ? CBD HEC 304 A 1 HETATM 41 C CGD HEC . . . L 11 -21.443 74.188 10.739 1 82.34 ? CGD HEC 304 A 1 HETATM 42 O O1D HEC . . . L 11 -21.015 74.744 11.783 1 91.07 ? O1D HEC 304 A 1 HETATM 43 O O2D HEC . . . L 11 -21.187 74.612 9.583 1 90.18 ? O2D HEC 304 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #