data_4D6T # _model_server_result.job_id RfIPwi7vtxTXjasLxdhFJg _model_server_result.datetime_utc '2024-11-05 14:07:11' _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 4d6t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":502}' # _entry.id 4D6T # _exptl.entry_id 4D6T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _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 4D6T _cell.length_a 129.896 _cell.length_b 129.896 _cell.length_c 722.152 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D6T _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS decameric 10 software_defined_assembly 1 PQS decameric 10 software_defined_assembly 2 # 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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA 1 1 K,L,M,N,O,P,Q,R,S,T,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA 2 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 ? 12 U N N ? 12 V N N ? 12 KA N N ? 12 LA 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 H SG CYS 37 H CYS 24 1_555 H SG CYS 81 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf2 H SG CYS 53 H CYS 40 1_555 H SG CYS 67 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? disulf ? disulf3 O SG CYS 222 R CYS 144 1_555 O SG CYS 238 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 R SG CYS 37 U CYS 24 1_555 R SG CYS 81 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf5 R SG CYS 53 U CYS 40 1_555 R SG CYS 67 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc5 D NE2 HIS 65 D HIS 41 1_555 Z FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc6 D SD MET 184 D MET 160 1_555 Z FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc7 M NE2 HIS 83 P HIS 83 1_555 KA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc8 M NE2 HIS 97 P HIS 97 1_555 LA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc9 M NE2 HIS 182 P HIS 182 1_555 KA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc10 M NE2 HIS 196 P HIS 196 1_555 LA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc11 N NE2 HIS 65 Q HIS 41 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc12 N SD MET 184 Q MET 160 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc13 O SG CYS 236 R CYS 158 1_555 TA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? # _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 530 n n CHA C4D HEM doub 531 n n CHA HHA HEM sing 532 n n CHB C4A HEM sing 533 n n CHB C1B HEM doub 534 n n CHB HHB HEM sing 535 n n CHC C4B HEM sing 536 n n CHC C1C HEM doub 537 n n CHC HHC HEM sing 538 n n CHD C4C HEM doub 539 n n CHD C1D HEM sing 540 n n CHD HHD HEM sing 541 n n C1A C2A HEM doub 542 n y C1A NA HEM sing 543 n y C2A C3A HEM sing 544 n y C2A CAA HEM sing 545 n n C3A C4A HEM doub 546 n y C3A CMA HEM sing 547 n n C4A NA HEM sing 548 n y CMA HMA HEM sing 549 n n CMA HMAA HEM sing 550 n n CMA HMAB HEM sing 551 n n CAA CBA HEM sing 552 n n CAA HAA HEM sing 553 n n CAA HAAA HEM sing 554 n n CBA CGA HEM sing 555 n n CBA HBA HEM sing 556 n n CBA HBAA HEM sing 557 n n CGA O1A HEM doub 558 n n CGA O2A HEM sing 559 n n C1B C2B HEM sing 560 n n C1B NB HEM sing 561 n n C2B C3B HEM doub 562 n n C2B CMB HEM sing 563 n n C3B C4B HEM sing 564 n n C3B CAB HEM sing 565 n n C4B NB HEM doub 566 n n CMB HMB HEM sing 567 n n CMB HMBA HEM sing 568 n n CMB HMBB HEM sing 569 n n CAB CBB HEM doub 570 n n CAB HAB HEM sing 571 n n CBB HBB HEM sing 572 n n CBB HBBA HEM sing 573 n n C1C C2C HEM sing 574 n y C1C NC HEM sing 575 n y C2C C3C HEM doub 576 n y C2C CMC HEM sing 577 n n C3C C4C HEM sing 578 n y C3C CAC HEM sing 579 n n C4C NC HEM sing 580 n y CMC HMC HEM sing 581 n n CMC HMCA HEM sing 582 n n CMC HMCB HEM sing 583 n n CAC CBC HEM doub 584 n n CAC HAC HEM sing 585 n n CBC HBC HEM sing 586 n n CBC HBCA HEM sing 587 n n C1D C2D HEM sing 588 n n C1D ND HEM doub 589 n n C2D C3D HEM doub 590 n n C2D CMD HEM sing 591 n n C3D C4D HEM sing 592 n n C3D CAD HEM sing 593 n n C4D ND HEM sing 594 n n CMD HMD HEM sing 595 n n CMD HMDA HEM sing 596 n n CMD HMDB HEM sing 597 n n CAD CBD HEM sing 598 n n CAD HAD HEM sing 599 n n CAD HADA HEM sing 600 n n CBD CGD HEM sing 601 n n CBD HBD HEM sing 602 n n CBD HBDA HEM sing 603 n n CGD O1D HEM doub 604 n n CGD O2D HEM sing 605 n n O2A H2A HEM sing 606 n n O2D H2D HEM sing 607 n n FE NA HEM sing 608 n n FE NB HEM sing 609 n n FE NC HEM sing 610 n n FE ND HEM sing 611 n n # _atom_sites.entry_id 4D6T _atom_sites.fract_transf_matrix[1][1] 0.007698 _atom_sites.fract_transf_matrix[1][2] 0.004445 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008889 _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] 0.001385 _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 U 12 HEM C 1 501 501 HEM HEM . V 12 HEM C 1 502 502 HEM HEM . W 13 4X9 C 1 503 503 4X9 4X9 . X 14 PO4 C 1 504 504 PO4 PO4 . Y 15 PEE C 1 505 505 PEE PEE . Z 16 HEC D 1 501 501 HEC HEC . AA 14 PO4 D 1 502 502 PO4 PO4 . BA 14 PO4 D 1 503 503 PO4 PO4 . CA 14 PO4 D 1 504 504 PO4 PO4 . DA 17 CDL D 1 505 505 CDL CDL . EA 15 PEE D 1 506 506 PEE PEE . FA 14 PO4 E 1 501 501 PO4 PO4 . GA 14 PO4 F 1 501 501 PO4 PO4 . HA 17 CDL G 1 501 501 CDL CDL . IA 14 PO4 N 1 501 501 PO4 PO4 . JA 14 PO4 N 1 1001 1001 PO4 PO4 . KA 12 HEM P 1 501 501 HEM HEM . LA 12 HEM P 1 502 502 HEM HEM . MA 13 4X9 P 1 503 503 4X9 4X9 . NA 15 PEE P 1 505 505 PEE PEE . OA 16 HEC Q 1 501 501 HEC HEC . PA 17 CDL Q 1 505 505 CDL CDL . QA 15 PEE Q 1 506 506 PEE PEE . RA 14 PO4 Q 1 1001 1001 PO4 PO4 . SA 14 PO4 Q 1 1002 1002 PO4 PO4 . TA 18 FES R 1 501 501 FES FES . UA 19 GOL R 1 502 502 GOL GOL . VA 14 PO4 S 1 501 501 PO4 PO4 . WA 17 CDL T 1 501 501 CDL CDL . # 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 . . . LA 12 30.236 20.05 -5.096 1 74.31 ? CHA HEM 502 P 1 HETATM 2 C CHB HEM . . . LA 12 29.641 20.595 -0.342 1 89.58 ? CHB HEM 502 P 1 HETATM 3 C CHC HEM . . . LA 12 26.372 17.03 -0.375 1 93.52 ? CHC HEM 502 P 1 HETATM 4 C CHD HEM . . . LA 12 27.557 16.021 -4.95 1 86.14 ? CHD HEM 502 P 1 HETATM 5 C C1A HEM . . . LA 12 30.261 20.538 -3.829 1 77.38 ? C1A HEM 502 P 1 HETATM 6 C C2A HEM . . . LA 12 30.84 21.756 -3.453 1 81.56 ? C2A HEM 502 P 1 HETATM 7 C C3A HEM . . . LA 12 30.668 21.904 -2.129 1 77.96 ? C3A HEM 502 P 1 HETATM 8 C C4A HEM . . . LA 12 30.018 20.776 -1.651 1 86.77 ? C4A HEM 502 P 1 HETATM 9 C CMA HEM . . . LA 12 31.127 23.049 -1.294 1 77.77 ? CMA HEM 502 P 1 HETATM 10 C CAA HEM . . . LA 12 31.486 22.763 -4.356 1 96.11 ? CAA HEM 502 P 1 HETATM 11 C CBA HEM . . . LA 12 30.424 23.864 -4.623 1 100.01 ? CBA HEM 502 P 1 HETATM 12 C CGA HEM . . . LA 12 29.372 23.499 -5.664 1 97.68 ? CGA HEM 502 P 1 HETATM 13 O O1A HEM . . . LA 12 28.132 23.552 -5.386 1 87.15 ? O1A HEM 502 P 1 HETATM 14 O O2A HEM . . . LA 12 29.751 23.176 -6.826 1 89.75 ? O2A HEM 502 P 1 HETATM 15 C C1B HEM . . . LA 12 28.689 19.654 0.027 1 91.12 ? C1B HEM 502 P 1 HETATM 16 C C2B HEM . . . LA 12 28.176 19.616 1.348 1 97.41 ? C2B HEM 502 P 1 HETATM 17 C C3B HEM . . . LA 12 27.246 18.623 1.378 1 97.41 ? C3B HEM 502 P 1 HETATM 18 C C4B HEM . . . LA 12 27.209 18.073 0.001 1 91.82 ? C4B HEM 502 P 1 HETATM 19 C CMB HEM . . . LA 12 28.601 20.503 2.494 1 106.45 ? CMB HEM 502 P 1 HETATM 20 C CAB HEM . . . LA 12 26.466 18.111 2.524 1 105.16 ? CAB HEM 502 P 1 HETATM 21 C CBB HEM . . . LA 12 26.746 18.402 3.799 1 106.08 ? CBB HEM 502 P 1 HETATM 22 C C1C HEM . . . LA 12 26.378 16.443 -1.63 1 91.84 ? C1C HEM 502 P 1 HETATM 23 C C2C HEM . . . LA 12 25.573 15.361 -2 1 90.87 ? C2C HEM 502 P 1 HETATM 24 C C3C HEM . . . LA 12 25.879 15.035 -3.309 1 86.24 ? C3C HEM 502 P 1 HETATM 25 C C4C HEM . . . LA 12 26.936 15.935 -3.727 1 84.01 ? C4C HEM 502 P 1 HETATM 26 C CMC HEM . . . LA 12 24.54 14.672 -1.131 1 88.62 ? CMC HEM 502 P 1 HETATM 27 C CAC HEM . . . LA 12 25.187 13.893 -3.947 1 82.94 ? CAC HEM 502 P 1 HETATM 28 C CBC HEM . . . LA 12 25.556 13.364 -5.091 1 85.87 ? CBC HEM 502 P 1 HETATM 29 C C1D HEM . . . LA 12 28.385 17.08 -5.332 1 89.8 ? C1D HEM 502 P 1 HETATM 30 C C2D HEM . . . LA 12 28.875 17.216 -6.722 1 98.29 ? C2D HEM 502 P 1 HETATM 31 C C3D HEM . . . LA 12 29.621 18.327 -6.797 1 91.6 ? C3D HEM 502 P 1 HETATM 32 C C4D HEM . . . LA 12 29.581 18.885 -5.423 1 80.92 ? C4D HEM 502 P 1 HETATM 33 C CMD HEM . . . LA 12 28.632 16.301 -7.897 1 104.55 ? CMD HEM 502 P 1 HETATM 34 C CAD HEM . . . LA 12 30.31 18.774 -8.09 1 91.55 ? CAD HEM 502 P 1 HETATM 35 C CBD HEM . . . LA 12 30.318 20.29 -8.346 1 98.33 ? CBD HEM 502 P 1 HETATM 36 C CGD HEM . . . LA 12 30.268 20.592 -9.824 1 95.03 ? CGD HEM 502 P 1 HETATM 37 O O1D HEM . . . LA 12 29.176 20.779 -10.409 1 85.33 ? O1D HEM 502 P 1 HETATM 38 O O2D HEM . . . LA 12 31.343 20.667 -10.457 1 98.77 ? O2D HEM 502 P 1 HETATM 39 N NA HEM . . . LA 12 29.73 19.963 -2.71 1 85.08 ? NA HEM 502 P 1 HETATM 40 N NB HEM . . . LA 12 28.081 18.75 -0.745 1 86.82 ? NB HEM 502 P 1 HETATM 41 N NC HEM . . . LA 12 27.19 16.775 -2.668 1 84.4 ? NC HEM 502 P 1 HETATM 42 N ND HEM . . . LA 12 28.814 18.122 -4.613 1 83.9 ? ND HEM 502 P 1 HETATM 43 FE FE HEM . . . LA 12 28.5 18.394 -2.781 1 81.68 ? FE HEM 502 P 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #