data_5OKD # _model_server_result.job_id 09TT9bmDuqNlQ8x6ATmaZg _model_server_result.datetime_utc '2024-11-23 10:36:43' _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":"N","auth_seq_id":402}' # _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 . . . N 14 -48.118 -81.033 33.118 1 71.86 ? CHA HEM 402 C 1 HETATM 2 C CHB HEM . . . N 14 -51.383 -78.119 35.164 1 71.11 ? CHB HEM 402 C 1 HETATM 3 C CHC HEM . . . N 14 -54.699 -79.617 31.928 1 69.74 ? CHC HEM 402 C 1 HETATM 4 C CHD HEM . . . N 14 -51.471 -82.692 30.086 1 70.2 ? CHD HEM 402 C 1 HETATM 5 C C1A HEM . . . N 14 -48.718 -80.1 33.921 1 71.86 ? C1A HEM 402 C 1 HETATM 6 C C2A HEM . . . N 14 -48.057 -79.391 34.955 1 73.03 ? C2A HEM 402 C 1 HETATM 7 C C3A HEM . . . N 14 -48.968 -78.568 35.535 1 72.34 ? C3A HEM 402 C 1 HETATM 8 C C4A HEM . . . N 14 -50.204 -78.779 34.87 1 71.25 ? C4A HEM 402 C 1 HETATM 9 C CMA HEM . . . N 14 -48.691 -77.61 36.676 1 72.49 ? CMA HEM 402 C 1 HETATM 10 C CAA HEM . . . N 14 -46.593 -79.492 35.315 1 74.73 ? CAA HEM 402 C 1 HETATM 11 C CBA HEM . . . N 14 -45.829 -78.628 34.303 1 75.72 ? CBA HEM 402 C 1 HETATM 12 C CGA HEM . . . N 14 -44.344 -78.848 34.426 1 77.8 ? CGA HEM 402 C 1 HETATM 13 O O1A HEM . . . N 14 -43.746 -78.496 35.468 1 79.5 ? O1A HEM 402 C 1 HETATM 14 O O2A HEM . . . N 14 -43.699 -79.37 33.488 1 77.39 ? O2A HEM 402 C 1 HETATM 15 C C1B HEM . . . N 14 -52.584 -78.261 34.445 1 70.71 ? C1B HEM 402 C 1 HETATM 16 C C2B HEM . . . N 14 -53.775 -77.527 34.754 1 70 ? C2B HEM 402 C 1 HETATM 17 C C3B HEM . . . N 14 -54.73 -77.929 33.849 1 70.23 ? C3B HEM 402 C 1 HETATM 18 C C4B HEM . . . N 14 -54.062 -78.945 32.982 1 69.86 ? C4B HEM 402 C 1 HETATM 19 C CMB HEM . . . N 14 -53.937 -76.504 35.862 1 69.14 ? CMB HEM 402 C 1 HETATM 20 C CAB HEM . . . N 14 -56.159 -77.531 33.717 1 71.68 ? CAB HEM 402 C 1 HETATM 21 C CBB HEM . . . N 14 -56.856 -76.77 34.565 1 72.4 ? CBB HEM 402 C 1 HETATM 22 C C1C HEM . . . N 14 -54.125 -80.6 31.12 1 69.55 ? C1C HEM 402 C 1 HETATM 23 C C2C HEM . . . N 14 -54.784 -81.348 30.112 1 69.21 ? C2C HEM 402 C 1 HETATM 24 C C3C HEM . . . N 14 -53.852 -82.248 29.581 1 69.42 ? C3C HEM 402 C 1 HETATM 25 C C4C HEM . . . N 14 -52.633 -82.009 30.292 1 69.33 ? C4C HEM 402 C 1 HETATM 26 C CMC HEM . . . N 14 -56.228 -81.182 29.686 1 68.66 ? CMC HEM 402 C 1 HETATM 27 C CAC HEM . . . N 14 -53.994 -83.259 28.488 1 68.88 ? CAC HEM 402 C 1 HETATM 28 C CBC HEM . . . N 14 -55.092 -83.536 27.8 1 68.67 ? CBC HEM 402 C 1 HETATM 29 C C1D HEM . . . N 14 -50.306 -82.453 30.794 1 70.75 ? C1D HEM 402 C 1 HETATM 30 C C2D HEM . . . N 14 -49.08 -83.199 30.47 1 71.64 ? C2D HEM 402 C 1 HETATM 31 C C3D HEM . . . N 14 -48.142 -82.741 31.306 1 72 ? C3D HEM 402 C 1 HETATM 32 C C4D HEM . . . N 14 -48.807 -81.714 32.134 1 71.21 ? C4D HEM 402 C 1 HETATM 33 C CMD HEM . . . N 14 -48.863 -84.274 29.425 1 72.22 ? CMD HEM 402 C 1 HETATM 34 C CAD HEM . . . N 14 -46.709 -83.235 31.352 1 72.8 ? CAD HEM 402 C 1 HETATM 35 C CBD HEM . . . N 14 -45.806 -82.411 30.433 1 73.42 ? CBD HEM 402 C 1 HETATM 36 C CGD HEM . . . N 14 -45.224 -81.234 31.179 1 74.22 ? CGD HEM 402 C 1 HETATM 37 O O1D HEM . . . N 14 -44.627 -81.443 32.255 1 74.96 ? O1D HEM 402 C 1 HETATM 38 O O2D HEM . . . N 14 -45.331 -80.057 30.748 1 73.71 ? O2D HEM 402 C 1 HETATM 39 N NA HEM . . . N 14 -50.038 -79.725 33.893 1 70.74 ? NA HEM 402 C 1 HETATM 40 N NB HEM . . . N 14 -52.801 -79.071 33.401 1 69.97 ? NB HEM 402 C 1 HETATM 41 N NC HEM . . . N 14 -52.839 -81.038 31.224 1 69 ? NC HEM 402 C 1 HETATM 42 N ND HEM . . . N 14 -50.103 -81.568 31.788 1 70.98 ? ND HEM 402 C 1 HETATM 43 FE FE HEM . . . N 14 -51.385 -80.39 32.573 1 68.99 ? FE HEM 402 C 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #