data_6XVF # _model_server_result.job_id REF5VmXWvQorwigHwKhmJA _model_server_result.datetime_utc '2024-11-27 06:06:52' _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 6xvf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":401}' # _entry.id 6XVF # _exptl.entry_id 6XVF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 15 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 2 _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 6XVF _cell.length_a 209.869 _cell.length_b 209.869 _cell.length_c 342.418 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XVF _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 eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,QA,RA _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' 10_445 -y-1,-x-1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -104.9345 -181.751885 57.069667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 15 P N N ? 15 Q 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 E SG CYS 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 H SG CYS 11 H CYS 24 1_555 H SG CYS 55 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 H SG CYS 27 H CYS 40 1_555 H SG CYS 41 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 C NE2 HIS 82 C HIS 83 1_555 P FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc2 C NE2 HIS 96 C HIS 97 1_555 Q FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 C NE2 HIS 181 C HIS 182 1_555 P FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc4 C NE2 HIS 195 C HIS 196 1_555 Q FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 D NE2 HIS 40 D HIS 41 1_555 Y FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc6 D SD MET 159 D MET 160 1_555 Y FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc7 E SG CYS 158 E CYS 158 1_555 BA FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? # _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 531 n n CHA C4D HEM doub 532 n n CHA HHA HEM sing 533 n n CHB C4A HEM sing 534 n n CHB C1B HEM doub 535 n n CHB HHB HEM sing 536 n n CHC C4B HEM sing 537 n n CHC C1C HEM doub 538 n n CHC HHC HEM sing 539 n n CHD C4C HEM doub 540 n n CHD C1D HEM sing 541 n n CHD HHD HEM sing 542 n n C1A C2A HEM doub 543 n y C1A NA HEM sing 544 n y C2A C3A HEM sing 545 n y C2A CAA HEM sing 546 n n C3A C4A HEM doub 547 n y C3A CMA HEM sing 548 n n C4A NA HEM sing 549 n y CMA HMA HEM sing 550 n n CMA HMAA HEM sing 551 n n CMA HMAB HEM sing 552 n n CAA CBA HEM sing 553 n n CAA HAA HEM sing 554 n n CAA HAAA HEM sing 555 n n CBA CGA HEM sing 556 n n CBA HBA HEM sing 557 n n CBA HBAA HEM sing 558 n n CGA O1A HEM doub 559 n n CGA O2A HEM sing 560 n n C1B C2B HEM sing 561 n n C1B NB HEM sing 562 n n C2B C3B HEM doub 563 n n C2B CMB HEM sing 564 n n C3B C4B HEM sing 565 n n C3B CAB HEM sing 566 n n C4B NB HEM doub 567 n n CMB HMB HEM sing 568 n n CMB HMBA HEM sing 569 n n CMB HMBB HEM sing 570 n n CAB CBB HEM doub 571 n n CAB HAB HEM sing 572 n n CBB HBB HEM sing 573 n n CBB HBBA HEM sing 574 n n C1C C2C HEM sing 575 n y C1C NC HEM sing 576 n y C2C C3C HEM doub 577 n y C2C CMC HEM sing 578 n n C3C C4C HEM sing 579 n y C3C CAC HEM sing 580 n n C4C NC HEM sing 581 n y CMC HMC HEM sing 582 n n CMC HMCA HEM sing 583 n n CMC HMCB HEM sing 584 n n CAC CBC HEM doub 585 n n CAC HAC HEM sing 586 n n CBC HBC HEM sing 587 n n CBC HBCA HEM sing 588 n n C1D C2D HEM sing 589 n n C1D ND HEM doub 590 n n C2D C3D HEM doub 591 n n C2D CMD HEM sing 592 n n C3D C4D HEM sing 593 n n C3D CAD HEM sing 594 n n C4D ND HEM sing 595 n n CMD HMD HEM sing 596 n n CMD HMDA HEM sing 597 n n CMD HMDB HEM sing 598 n n CAD CBD HEM sing 599 n n CAD HAD HEM sing 600 n n CAD HADA HEM sing 601 n n CBD CGD HEM sing 602 n n CBD HBD HEM sing 603 n n CBD HBDA HEM sing 604 n n CGD O1D HEM doub 605 n n CGD O2D HEM sing 606 n n O2A H2A HEM sing 607 n n O2D H2D HEM sing 608 n n FE NA HEM sing 609 n n FE NB HEM sing 610 n n FE NC HEM sing 611 n n FE ND HEM sing 612 n n # _atom_sites.entry_id 6XVF _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] 0.00292 _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 1 501 501 PG4 PG4 . L 12 6PE A 1 502 502 6PE 6PE . M 13 PO4 A 1 503 503 PO4 PO4 . N 14 CDL A 1 504 401 CDL CDL . O 13 PO4 B 1 501 501 PO4 PO4 . P 15 HEM C 1 401 402 HEM HEM . Q 15 HEM C 1 402 403 HEM HEM . R 16 LMT C 1 403 405 LMT LMT . S 11 PG4 C 1 404 406 PG4 PG4 . T 11 PG4 C 1 405 407 PG4 PG4 . U 14 CDL C 1 406 408 CDL CDL . V 17 PEE C 1 407 409 PEE PEE . W 18 JAG C 1 408 404 JAG JAG . X 13 PO4 C 1 409 410 PO4 PO4 . Y 19 HEC D 1 501 501 HEC HEC . Z 13 PO4 D 1 502 502 PO4 PO4 . AA 14 CDL D 1 503 503 CDL CDL . BA 20 FES E 1 201 201 FES FES . CA 21 PX4 E 1 202 202 PX4 PX4 . DA 13 PO4 E 1 203 203 PO4 PO4 . EA 17 PEE E 1 204 204 PEE PEE . FA 14 CDL E 1 205 205 CDL CDL . GA 13 PO4 F 1 501 501 PO4 PO4 . HA 13 PO4 G 1 101 101 PO4 PO4 . IA 13 PO4 G 1 102 102 PO4 PO4 . JA 13 PO4 G 1 103 103 PO4 PO4 . KA 22 HOH A 1 601 504 HOH HOH . KA 22 HOH A 2 602 508 HOH HOH . KA 22 HOH A 3 603 507 HOH HOH . KA 22 HOH A 4 604 505 HOH HOH . KA 22 HOH A 5 605 509 HOH HOH . KA 22 HOH A 6 606 506 HOH HOH . LA 22 HOH B 1 601 502 HOH HOH . LA 22 HOH B 2 602 503 HOH HOH . MA 22 HOH C 1 501 412 HOH HOH . MA 22 HOH C 2 502 414 HOH HOH . MA 22 HOH C 3 503 411 HOH HOH . MA 22 HOH C 4 504 413 HOH HOH . NA 22 HOH D 1 601 505 HOH HOH . NA 22 HOH D 2 602 504 HOH HOH . OA 22 HOH F 1 601 502 HOH HOH . PA 22 HOH G 1 201 104 HOH HOH . QA 22 HOH I 1 101 101 HOH HOH . QA 22 HOH I 2 102 102 HOH HOH . RA 22 HOH J 1 101 101 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 . . . P 15 -48.279 -81.044 33.103 1 134.22 ? CHA HEM 401 C 1 HETATM 2 C CHB HEM . . . P 15 -51.495 -78.124 35.186 1 132.12 ? CHB HEM 401 C 1 HETATM 3 C CHC HEM . . . P 15 -54.804 -79.502 31.905 1 130.76 ? CHC HEM 401 C 1 HETATM 4 C CHD HEM . . . P 15 -51.636 -82.642 30.058 1 132.88 ? CHD HEM 401 C 1 HETATM 5 C C1A HEM . . . P 15 -48.873 -80.112 33.918 1 133.47 ? C1A HEM 401 C 1 HETATM 6 C C2A HEM . . . P 15 -48.189 -79.393 34.92 1 134.05 ? C2A HEM 401 C 1 HETATM 7 C C3A HEM . . . P 15 -49.082 -78.56 35.516 1 133.37 ? C3A HEM 401 C 1 HETATM 8 C C4A HEM . . . P 15 -50.323 -78.777 34.879 1 132.47 ? C4A HEM 401 C 1 HETATM 9 C CMA HEM . . . P 15 -48.803 -77.593 36.649 1 133.71 ? CMA HEM 401 C 1 HETATM 10 C CAA HEM . . . P 15 -46.723 -79.512 35.237 1 135.21 ? CAA HEM 401 C 1 HETATM 11 C CBA HEM . . . P 15 -46.044 -78.544 34.272 1 136.73 ? CBA HEM 401 C 1 HETATM 12 C CGA HEM . . . P 15 -44.564 -78.689 34.369 1 138.71 ? CGA HEM 401 C 1 HETATM 13 O O1A HEM . . . P 15 -43.963 -78.394 35.432 1 140.09 ? O1A HEM 401 C 1 HETATM 14 O O2A HEM . . . P 15 -43.948 -79.092 33.365 1 139.55 ? O2A HEM 401 C 1 HETATM 15 C C1B HEM . . . P 15 -52.67 -78.247 34.435 1 131.27 ? C1B HEM 401 C 1 HETATM 16 C C2B HEM . . . P 15 -53.838 -77.493 34.759 1 130.69 ? C2B HEM 401 C 1 HETATM 17 C C3B HEM . . . P 15 -54.8 -77.865 33.862 1 130.55 ? C3B HEM 401 C 1 HETATM 18 C C4B HEM . . . P 15 -54.148 -78.878 32.972 1 130.78 ? C4B HEM 401 C 1 HETATM 19 C CMB HEM . . . P 15 -53.966 -76.489 35.887 1 130.4 ? CMB HEM 401 C 1 HETATM 20 C CAB HEM . . . P 15 -56.2 -77.371 33.767 1 130.13 ? CAB HEM 401 C 1 HETATM 21 C CBB HEM . . . P 15 -56.855 -76.798 34.781 1 129.76 ? CBB HEM 401 C 1 HETATM 22 C C1C HEM . . . P 15 -54.248 -80.496 31.106 1 131.06 ? C1C HEM 401 C 1 HETATM 23 C C2C HEM . . . P 15 -54.908 -81.235 30.088 1 131.28 ? C2C HEM 401 C 1 HETATM 24 C C3C HEM . . . P 15 -53.97 -82.141 29.575 1 131.71 ? C3C HEM 401 C 1 HETATM 25 C C4C HEM . . . P 15 -52.769 -81.924 30.296 1 131.94 ? C4C HEM 401 C 1 HETATM 26 C CMC HEM . . . P 15 -56.354 -81.062 29.649 1 130.46 ? CMC HEM 401 C 1 HETATM 27 C CAC HEM . . . P 15 -54.077 -83.16 28.497 1 131.43 ? CAC HEM 401 C 1 HETATM 28 C CBC HEM . . . P 15 -55.165 -83.375 27.781 1 130.65 ? CBC HEM 401 C 1 HETATM 29 C C1D HEM . . . P 15 -50.455 -82.424 30.746 1 133.25 ? C1D HEM 401 C 1 HETATM 30 C C2D HEM . . . P 15 -49.239 -83.191 30.41 1 133.78 ? C2D HEM 401 C 1 HETATM 31 C C3D HEM . . . P 15 -48.299 -82.749 31.253 1 134.25 ? C3D HEM 401 C 1 HETATM 32 C C4D HEM . . . P 15 -48.957 -81.719 32.097 1 133.85 ? C4D HEM 401 C 1 HETATM 33 C CMD HEM . . . P 15 -49.064 -84.254 29.347 1 133.58 ? CMD HEM 401 C 1 HETATM 34 C CAD HEM . . . P 15 -46.867 -83.231 31.287 1 135.28 ? CAD HEM 401 C 1 HETATM 35 C CBD HEM . . . P 15 -46.028 -82.338 30.361 1 136.2 ? CBD HEM 401 C 1 HETATM 36 C CGD HEM . . . P 15 -45.453 -81.155 31.121 1 137.18 ? CGD HEM 401 C 1 HETATM 37 O O1D HEM . . . P 15 -44.821 -81.35 32.19 1 137.91 ? O1D HEM 401 C 1 HETATM 38 O O2D HEM . . . P 15 -45.594 -79.979 30.697 1 137.11 ? O2D HEM 401 C 1 HETATM 39 N NA HEM . . . P 15 -50.189 -79.737 33.919 1 132.26 ? NA HEM 401 C 1 HETATM 40 N NB HEM . . . P 15 -52.885 -79.049 33.383 1 130.88 ? NB HEM 401 C 1 HETATM 41 N NC HEM . . . P 15 -52.972 -80.957 31.241 1 131.3 ? NC HEM 401 C 1 HETATM 42 N ND HEM . . . P 15 -50.247 -81.558 31.755 1 132.94 ? ND HEM 401 C 1 HETATM 43 FE FE HEM . . . P 15 -51.47 -80.356 32.546 1 130.99 ? FE HEM 401 C 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #