data_5OKD # _model_server_result.job_id S0O4MLyUwmPth2T74i1NYw _model_server_result.datetime_utc '2024-11-23 10:47:03' _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":"O","auth_seq_id":403}' # _entry.id 5OKD # _exptl.entry_id 5OKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 14 _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 14 N N N ? 14 O 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 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 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 582 n n CHA C4D HEM doub 583 n n CHA HHA HEM sing 584 n n CHB C4A HEM sing 585 n n CHB C1B HEM doub 586 n n CHB HHB HEM sing 587 n n CHC C4B HEM sing 588 n n CHC C1C HEM doub 589 n n CHC HHC HEM sing 590 n n CHD C4C HEM doub 591 n n CHD C1D HEM sing 592 n n CHD HHD HEM sing 593 n n C1A C2A HEM doub 594 n y C1A NA HEM sing 595 n y C2A C3A HEM sing 596 n y C2A CAA HEM sing 597 n n C3A C4A HEM doub 598 n y C3A CMA HEM sing 599 n n C4A NA HEM sing 600 n y CMA HMA HEM sing 601 n n CMA HMAA HEM sing 602 n n CMA HMAB HEM sing 603 n n CAA CBA HEM sing 604 n n CAA HAA HEM sing 605 n n CAA HAAA HEM sing 606 n n CBA CGA HEM sing 607 n n CBA HBA HEM sing 608 n n CBA HBAA HEM sing 609 n n CGA O1A HEM doub 610 n n CGA O2A HEM sing 611 n n C1B C2B HEM sing 612 n n C1B NB HEM sing 613 n n C2B C3B HEM doub 614 n n C2B CMB HEM sing 615 n n C3B C4B HEM sing 616 n n C3B CAB HEM sing 617 n n C4B NB HEM doub 618 n n CMB HMB HEM sing 619 n n CMB HMBA HEM sing 620 n n CMB HMBB HEM sing 621 n n CAB CBB HEM doub 622 n n CAB HAB HEM sing 623 n n CBB HBB HEM sing 624 n n CBB HBBA HEM sing 625 n n C1C C2C HEM sing 626 n y C1C NC HEM sing 627 n y C2C C3C HEM doub 628 n y C2C CMC HEM sing 629 n n C3C C4C HEM sing 630 n y C3C CAC HEM sing 631 n n C4C NC HEM sing 632 n y CMC HMC HEM sing 633 n n CMC HMCA HEM sing 634 n n CMC HMCB HEM sing 635 n n CAC CBC HEM doub 636 n n CAC HAC HEM sing 637 n n CBC HBC HEM sing 638 n n CBC HBCA HEM sing 639 n n C1D C2D HEM sing 640 n n C1D ND HEM doub 641 n n C2D C3D HEM doub 642 n n C2D CMD HEM sing 643 n n C3D C4D HEM sing 644 n n C3D CAD HEM sing 645 n n C4D ND HEM sing 646 n n CMD HMD HEM sing 647 n n CMD HMDA HEM sing 648 n n CMD HMDB HEM sing 649 n n CAD CBD HEM sing 650 n n CAD HAD HEM sing 651 n n CAD HADA HEM sing 652 n n CBD CGD HEM sing 653 n n CBD HBD HEM sing 654 n n CBD HBDA HEM sing 655 n n CGD O1D HEM doub 656 n n CGD O2D HEM sing 657 n n O2A H2A HEM sing 658 n n O2D H2D HEM sing 659 n n FE NA HEM sing 660 n n FE NB HEM sing 661 n n FE NC HEM sing 662 n n FE ND HEM sing 663 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 C CHA HEM . . . O 14 -68.435 -65.127 38.051 1 64.74 ? CHA HEM 403 C 1 HETATM 2 C CHB HEM . . . O 14 -65.862 -68.355 35.545 1 65.6 ? CHB HEM 403 C 1 HETATM 3 C CHC HEM . . . O 14 -64.006 -70.019 39.697 1 65.47 ? CHC HEM 403 C 1 HETATM 4 C CHD HEM . . . O 14 -67.121 -67.272 42.148 1 65.35 ? CHD HEM 403 C 1 HETATM 5 C C1A HEM . . . O 14 -67.83 -65.803 37.029 1 64.79 ? C1A HEM 403 C 1 HETATM 6 C C2A HEM . . . O 14 -67.907 -65.426 35.673 1 65.26 ? C2A HEM 403 C 1 HETATM 7 C C3A HEM . . . O 14 -67.189 -66.329 34.961 1 65.27 ? C3A HEM 403 C 1 HETATM 8 C C4A HEM . . . O 14 -66.675 -67.281 35.873 1 65.05 ? C4A HEM 403 C 1 HETATM 9 C CMA HEM . . . O 14 -67.011 -66.279 33.46 1 65.97 ? CMA HEM 403 C 1 HETATM 10 C CAA HEM . . . O 14 -68.616 -64.216 35.103 1 65.87 ? CAA HEM 403 C 1 HETATM 11 C CBA HEM . . . O 14 -67.608 -63.062 34.913 1 67.28 ? CBA HEM 403 C 1 HETATM 12 C CGA HEM . . . O 14 -67.011 -62.527 36.198 1 67.78 ? CGA HEM 403 C 1 HETATM 13 O O1A HEM . . . O 14 -65.832 -62.784 36.501 1 67.85 ? O1A HEM 403 C 1 HETATM 14 O O2A HEM . . . O 14 -67.667 -61.795 36.966 1 68.77 ? O2A HEM 403 C 1 HETATM 15 C C1B HEM . . . O 14 -65.111 -69.096 36.464 1 64.49 ? C1B HEM 403 C 1 HETATM 16 C C2B HEM . . . O 14 -64.142 -70.073 36.074 1 63.52 ? C2B HEM 403 C 1 HETATM 17 C C3B HEM . . . O 14 -63.593 -70.549 37.24 1 65.14 ? C3B HEM 403 C 1 HETATM 18 C C4B HEM . . . O 14 -64.278 -69.815 38.338 1 65.5 ? C4B HEM 403 C 1 HETATM 19 C CMB HEM . . . O 14 -63.799 -70.485 34.657 1 62.17 ? CMB HEM 403 C 1 HETATM 20 C CAB HEM . . . O 14 -62.581 -71.604 37.485 1 66.38 ? CAB HEM 403 C 1 HETATM 21 C CBB HEM . . . O 14 -62.148 -72.48 36.585 1 68.26 ? CBB HEM 403 C 1 HETATM 22 C C1C HEM . . . O 14 -64.659 -69.409 40.762 1 64.87 ? C1C HEM 403 C 1 HETATM 23 C C2C HEM . . . O 14 -64.348 -69.587 42.125 1 64.86 ? C2C HEM 403 C 1 HETATM 24 C C3C HEM . . . O 14 -65.238 -68.791 42.845 1 65.6 ? C3C HEM 403 C 1 HETATM 25 C C4C HEM . . . O 14 -66.101 -68.158 41.879 1 65.03 ? C4C HEM 403 C 1 HETATM 26 C CMC HEM . . . O 14 -63.235 -70.456 42.665 1 65.06 ? CMC HEM 403 C 1 HETATM 27 C CAC HEM . . . O 14 -65.38 -68.62 44.317 1 66.03 ? CAC HEM 403 C 1 HETATM 28 C CBC HEM . . . O 14 -64.714 -69.236 45.294 1 66.73 ? CBC HEM 403 C 1 HETATM 29 C C1D HEM . . . O 14 -67.719 -66.468 41.187 1 65.18 ? C1D HEM 403 C 1 HETATM 30 C C2D HEM . . . O 14 -68.653 -65.384 41.567 1 64.65 ? C2D HEM 403 C 1 HETATM 31 C C3D HEM . . . O 14 -69.011 -64.785 40.431 1 64.67 ? C3D HEM 403 C 1 HETATM 32 C C4D HEM . . . O 14 -68.289 -65.499 39.368 1 64.66 ? C4D HEM 403 C 1 HETATM 33 C CMD HEM . . . O 14 -69.125 -65.02 42.954 1 65.3 ? CMD HEM 403 C 1 HETATM 34 C CAD HEM . . . O 14 -69.966 -63.623 40.283 1 66.03 ? CAD HEM 403 C 1 HETATM 35 C CBD HEM . . . O 14 -69.19 -62.314 40.308 1 66.54 ? CBD HEM 403 C 1 HETATM 36 C CGD HEM . . . O 14 -70.111 -61.129 40.333 1 66.04 ? CGD HEM 403 C 1 HETATM 37 O O1D HEM . . . O 14 -69.72 -60.058 40.844 1 65.92 ? O1D HEM 403 C 1 HETATM 38 O O2D HEM . . . O 14 -71.252 -61.198 39.839 1 65.7 ? O2D HEM 403 C 1 HETATM 39 N NA HEM . . . O 14 -67.058 -66.927 37.141 1 64.54 ? NA HEM 403 C 1 HETATM 40 N NB HEM . . . O 14 -65.15 -68.973 37.79 1 64.86 ? NB HEM 403 C 1 HETATM 41 N NC HEM . . . O 14 -65.702 -68.543 40.638 1 64.33 ? NC HEM 403 C 1 HETATM 42 N ND HEM . . . O 14 -67.531 -66.5 39.861 1 65.28 ? ND HEM 403 C 1 HETATM 43 FE FE HEM . . . O 14 -66.418 -67.698 38.867 1 63.3 ? FE HEM 403 C 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #