data_8KDE # _model_server_result.job_id 3zZTYMqXLea1BOSSNjPsYA _model_server_result.datetime_utc '2024-12-18 11:07:14' _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 8kde # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BB","auth_seq_id":101}' # _entry.id 8KDE # _exptl.entry_id 8KDE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 616.487 _entity.id 25 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 8KDE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KDE _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octadecameric _pdbx_struct_assembly.oligomeric_count 18 _pdbx_struct_assembly.details author_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,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC _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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 25 _struct_asym.id BB _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 B NE2 HIS 214 D HIS 214 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc2 B NE2 HIS 268 D HIS 268 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc3 C NE2 HIS 23 E HIS 23 1_555 BB FE HEM . E HEM 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc4 BB FE HEM . E HEM 101 1_555 D NE2 HIS 23 F HIS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc5 P OD1 ASN 27 C ASN 27 1_555 VB MG CLA . C CLA 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc6 Q NE2 HIS 215 A HIS 215 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc7 Q NE2 HIS 272 A HIS 272 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc8 EC O2 BCT . A BCT 401 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc9 EC O3 BCT . A BCT 401 1_555 FC FE FE2 . A FE2 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? # _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 538 n n CHA C4D HEM doub 539 n n CHA HHA HEM sing 540 n n CHB C4A HEM sing 541 n n CHB C1B HEM doub 542 n n CHB HHB HEM sing 543 n n CHC C4B HEM sing 544 n n CHC C1C HEM doub 545 n n CHC HHC HEM sing 546 n n CHD C4C HEM doub 547 n n CHD C1D HEM sing 548 n n CHD HHD HEM sing 549 n n C1A C2A HEM doub 550 n y C1A NA HEM sing 551 n y C2A C3A HEM sing 552 n y C2A CAA HEM sing 553 n n C3A C4A HEM doub 554 n y C3A CMA HEM sing 555 n n C4A NA HEM sing 556 n y CMA HMA HEM sing 557 n n CMA HMAA HEM sing 558 n n CMA HMAB HEM sing 559 n n CAA CBA HEM sing 560 n n CAA HAA HEM sing 561 n n CAA HAAA HEM sing 562 n n CBA CGA HEM sing 563 n n CBA HBA HEM sing 564 n n CBA HBAA HEM sing 565 n n CGA O1A HEM doub 566 n n CGA O2A HEM sing 567 n n C1B C2B HEM sing 568 n n C1B NB HEM sing 569 n n C2B C3B HEM doub 570 n n C2B CMB HEM sing 571 n n C3B C4B HEM sing 572 n n C3B CAB HEM sing 573 n n C4B NB HEM doub 574 n n CMB HMB HEM sing 575 n n CMB HMBA HEM sing 576 n n CMB HMBB HEM sing 577 n n CAB CBB HEM doub 578 n n CAB HAB HEM sing 579 n n CBB HBB HEM sing 580 n n CBB HBBA HEM sing 581 n n C1C C2C HEM sing 582 n y C1C NC HEM sing 583 n y C2C C3C HEM doub 584 n y C2C CMC HEM sing 585 n n C3C C4C HEM sing 586 n y C3C CAC HEM sing 587 n n C4C NC HEM sing 588 n y CMC HMC HEM sing 589 n n CMC HMCA HEM sing 590 n n CMC HMCB HEM sing 591 n n CAC CBC HEM doub 592 n n CAC HAC HEM sing 593 n n CBC HBC HEM sing 594 n n CBC HBCA HEM sing 595 n n C1D C2D HEM sing 596 n n C1D ND HEM doub 597 n n C2D C3D HEM doub 598 n n C2D CMD HEM sing 599 n n C3D C4D HEM sing 600 n n C3D CAD HEM sing 601 n n C4D ND HEM sing 602 n n CMD HMD HEM sing 603 n n CMD HMDA HEM sing 604 n n CMD HMDB HEM sing 605 n n CAD CBD HEM sing 606 n n CAD HAD HEM sing 607 n n CAD HADA HEM sing 608 n n CBD CGD HEM sing 609 n n CBD HBD HEM sing 610 n n CBD HBDA HEM sing 611 n n CGD O1D HEM doub 612 n n CGD O2D HEM sing 613 n n O2A H2A HEM sing 614 n n O2D H2D HEM sing 615 n n FE NA HEM sing 616 n n FE NB HEM sing 617 n n FE NC HEM sing 618 n n FE ND HEM sing 619 n n # _atom_sites.entry_id 8KDE _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 S 19 CLA B 1 601 602 CLA CLA . T 19 CLA B 1 602 603 CLA CLA . U 19 CLA B 1 603 604 CLA CLA . V 19 CLA B 1 604 605 CLA CLA . W 19 CLA B 1 605 606 CLA CLA . X 19 CLA B 1 606 607 CLA CLA . Y 19 CLA B 1 607 608 CLA CLA . Z 19 CLA B 1 608 609 CLA CLA . AA 19 CLA B 1 609 610 CLA CLA . BA 19 CLA B 1 610 611 CLA CLA . CA 19 CLA B 1 611 612 CLA CLA . DA 19 CLA B 1 612 613 CLA CLA . EA 19 CLA B 1 613 614 CLA CLA . FA 19 CLA B 1 614 615 CLA CLA . GA 19 CLA B 1 615 616 CLA CLA . HA 19 CLA B 1 616 617 CLA CLA . IA 20 BCR B 1 617 618 BCR BCR . JA 20 BCR B 1 618 619 BCR BCR . KA 20 BCR B 1 619 620 BCR BCR . LA 21 LMG B 1 620 622 LMG LMG . MA 22 LHG B 1 621 412 LHG LHG . NA 22 LHG B 1 622 413 LHG LHG . OA 21 LMG B 1 623 102 LMG LMG . PA 22 LHG B 1 624 201 LHG LHG . QA 19 CLA D 1 401 402 CLA CLA . RA 19 CLA D 1 402 403 CLA CLA . SA 20 BCR D 1 403 404 BCR BCR . TA 23 PL9 D 1 404 405 PL9 PL9 . UA 22 LHG D 1 405 408 LHG LHG . VA 22 LHG D 1 406 409 LHG LHG . WA 22 LHG D 1 407 410 LHG LHG . XA 21 LMG D 1 408 411 LMG LMG . YA 19 CLA D 1 409 406 CLA CLA . ZA 24 PHO D 1 410 408 PHO PHO . AB 24 PHO D 1 411 409 PHO PHO . BB 25 HEM E 1 101 101 HEM HEM . CB 20 BCR H 1 101 101 BCR BCR . DB 20 BCR K 1 101 516 BCR BCR . EB 21 LMG K 1 102 521 LMG LMG . FB 22 LHG K 1 103 419 LHG LHG . GB 22 LHG L 1 101 101 LHG LHG . HB 22 LHG X 1 201 414 LHG LHG . IB 26 VTQ X 1 202 102 VTQ VTQ . JB 20 BCR Z 1 101 514 BCR BCR . KB 21 LMG C 1 601 601 LMG LMG . LB 19 CLA C 1 602 501 CLA CLA . MB 19 CLA C 1 603 502 CLA CLA . NB 19 CLA C 1 604 503 CLA CLA . OB 19 CLA C 1 605 504 CLA CLA . PB 19 CLA C 1 606 505 CLA CLA . QB 19 CLA C 1 607 506 CLA CLA . RB 19 CLA C 1 608 507 CLA CLA . SB 19 CLA C 1 609 508 CLA CLA . TB 19 CLA C 1 610 509 CLA CLA . UB 19 CLA C 1 611 510 CLA CLA . VB 19 CLA C 1 612 511 CLA CLA . WB 19 CLA C 1 613 512 CLA CLA . XB 19 CLA C 1 614 513 CLA CLA . YB 20 BCR C 1 615 515 BCR BCR . ZB 20 BCR C 1 616 517 BCR BCR . AC 27 DGD C 1 617 518 DGD DGD . BC 27 DGD C 1 618 519 DGD DGD . CC 27 DGD C 1 619 520 DGD DGD . DC 28 SQD C 1 620 412 SQD SQD . EC 29 BCT A 1 401 401 BCT BCT . FC 30 FE2 A 1 402 402 FE2 FE2 . GC 19 CLA A 1 403 405 CLA CLA . HC 19 CLA A 1 404 407 CLA CLA . IC 19 CLA A 1 405 410 CLA CLA . JC 20 BCR A 1 406 411 BCR BCR . KC 21 LMG A 1 407 413 LMG LMG . LC 22 LHG A 1 408 415 LHG LHG . # 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 . . . BB 25 152.39 178.832 203.382 1 78.76 0 CHA HEM 101 E 1 HETATM 2 C CHB HEM . . . BB 25 148.398 181.544 203.713 1 78.76 0 CHB HEM 101 E 1 HETATM 3 C CHC HEM . . . BB 25 146.601 179.396 199.747 1 78.76 0 CHC HEM 101 E 1 HETATM 4 C CHD HEM . . . BB 25 150.435 176.411 199.665 1 78.76 0 CHD HEM 101 E 1 HETATM 5 C C1A HEM . . . BB 25 151.428 179.68 203.873 1 78.76 0 C1A HEM 101 E 1 HETATM 6 C C2A HEM . . . BB 25 151.415 180.295 205.181 1 78.76 0 C2A HEM 101 E 1 HETATM 7 C C3A HEM . . . BB 25 150.317 181.048 205.272 1 78.76 0 C3A HEM 101 E 1 HETATM 8 C C4A HEM . . . BB 25 149.589 180.93 204.027 1 78.76 0 C4A HEM 101 E 1 HETATM 9 C CMA HEM . . . BB 25 149.889 181.892 206.49 1 78.76 0 CMA HEM 101 E 1 HETATM 10 C CAA HEM . . . BB 25 152.496 180.112 206.266 1 78.76 0 CAA HEM 101 E 1 HETATM 11 C CBA HEM . . . BB 25 151.884 179.418 207.477 1 78.76 0 CBA HEM 101 E 1 HETATM 12 C CGA HEM . . . BB 25 152.95 179.199 208.514 1 78.76 0 CGA HEM 101 E 1 HETATM 13 O O1A HEM . . . BB 25 152.615 178.731 209.631 1 78.76 0 O1A HEM 101 E 1 HETATM 14 O O2A HEM . . . BB 25 154.136 179.498 208.222 1 78.76 0 O2A HEM 101 E 1 HETATM 15 C C1B HEM . . . BB 25 147.628 181.286 202.599 1 78.76 0 C1B HEM 101 E 1 HETATM 16 C C2B HEM . . . BB 25 146.576 182.132 202.086 1 78.76 0 C2B HEM 101 E 1 HETATM 17 C C3B HEM . . . BB 25 146.065 181.56 200.992 1 78.76 0 C3B HEM 101 E 1 HETATM 18 C C4B HEM . . . BB 25 146.789 180.315 200.762 1 78.76 0 C4B HEM 101 E 1 HETATM 19 C CMB HEM . . . BB 25 146.131 183.467 202.722 1 78.76 0 CMB HEM 101 E 1 HETATM 20 C CAB HEM . . . BB 25 144.906 182.181 200.174 1 78.76 0 CAB HEM 101 E 1 HETATM 21 C CBB HEM . . . BB 25 144.411 181.61 199.072 1 78.76 0 CBB HEM 101 E 1 HETATM 22 C C1C HEM . . . BB 25 147.473 178.384 199.395 1 78.76 0 C1C HEM 101 E 1 HETATM 23 C C2C HEM . . . BB 25 147.282 177.433 198.317 1 78.76 0 C2C HEM 101 E 1 HETATM 24 C C3C HEM . . . BB 25 148.338 176.607 198.295 1 78.76 0 C3C HEM 101 E 1 HETATM 25 C C4C HEM . . . BB 25 149.235 177.013 199.354 1 78.76 0 C4C HEM 101 E 1 HETATM 26 C CMC HEM . . . BB 25 146.053 177.413 197.382 1 78.76 0 CMC HEM 101 E 1 HETATM 27 C CAC HEM . . . BB 25 148.632 175.422 197.344 1 78.76 0 CAC HEM 101 E 1 HETATM 28 C CBC HEM . . . BB 25 147.897 175.167 196.257 1 78.76 0 CBC HEM 101 E 1 HETATM 29 C C1D HEM . . . BB 25 151.328 176.849 200.617 1 78.76 0 C1D HEM 101 E 1 HETATM 30 C C2D HEM . . . BB 25 152.685 176.377 200.806 1 78.76 0 C2D HEM 101 E 1 HETATM 31 C C3D HEM . . . BB 25 153.219 177.052 201.825 1 78.76 0 C3D HEM 101 E 1 HETATM 32 C C4D HEM . . . BB 25 152.222 177.965 202.329 1 78.76 0 C4D HEM 101 E 1 HETATM 33 C CMD HEM . . . BB 25 153.386 175.294 199.96 1 78.76 0 CMD HEM 101 E 1 HETATM 34 C CAD HEM . . . BB 25 154.639 176.912 202.41 1 78.76 0 CAD HEM 101 E 1 HETATM 35 C CBD HEM . . . BB 25 155.423 178.19 202.119 1 78.76 0 CBD HEM 101 E 1 HETATM 36 C CGD HEM . . . BB 25 156.367 178.524 203.247 1 78.76 0 CGD HEM 101 E 1 HETATM 37 O O1D HEM . . . BB 25 156.517 177.702 204.186 1 78.76 0 O1D HEM 101 E 1 HETATM 38 O O2D HEM . . . BB 25 156.977 179.624 203.206 1 78.76 0 O2D HEM 101 E 1 HETATM 39 N NA HEM . . . BB 25 150.298 180.087 203.195 1 78.76 0 NA HEM 101 E 1 HETATM 40 N NB HEM . . . BB 25 147.736 180.19 201.764 1 78.76 0 NB HEM 101 E 1 HETATM 41 N NC HEM . . . BB 25 148.675 178.093 200.008 1 78.76 0 NC HEM 101 E 1 HETATM 42 N ND HEM . . . BB 25 151.08 177.819 201.569 1 78.76 0 ND HEM 101 E 1 HETATM 43 FE FE HEM . . . BB 25 149.455 179.049 201.626 1 78.76 0 FE HEM 101 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #