data_3H1J # _model_server_result.job_id lSItjZadAbQCFex105K1oA _model_server_result.datetime_utc '2024-11-24 18:46:31' _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 3h1j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":501}' # _entry.id 3H1J # _exptl.entry_id 3H1J _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 90 _cell.entry_id 3H1J _cell.length_a 173.464 _cell.length_b 182.448 _cell.length_c 241.328 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H1J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB _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 ? 12 V N N ? 12 W N N ? 12 OA N N ? 12 PA 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf2 H SG CYS 23 H CYS 24 1_555 H SG CYS 67 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 H SG CYS 39 H CYS 40 1_555 H SG CYS 53 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 O SG CYS 144 R CYS 144 1_555 O SG CYS 160 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf5 R SG CYS 23 U CYS 24 1_555 R SG CYS 67 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 R SG CYS 39 U CYS 40 1_555 R SG CYS 53 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 C NE2 HIS 84 C HIS 84 1_555 V FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc2 C NE2 HIS 98 C HIS 98 1_555 W FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 V FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 W FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc5 D NE2 HIS 41 D HIS 41 1_555 FA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc6 D SD MET 160 D MET 160 1_555 FA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc7 E SG CYS 139 E CYS 139 1_555 HA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc8 E ND1 HIS 141 E HIS 141 1_555 HA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc9 E SG CYS 158 E CYS 158 1_555 HA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc10 E ND1 HIS 161 E HIS 161 1_555 HA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc11 M NE2 HIS 84 P HIS 84 1_555 OA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc12 M NE2 HIS 98 P HIS 98 1_555 PA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc13 M NE2 HIS 183 P HIS 183 1_555 OA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc14 M NE2 HIS 197 P HIS 197 1_555 PA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc15 N NE2 HIS 41 Q HIS 41 1_555 YA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc16 N SD MET 160 Q MET 160 1_555 YA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc17 O SG CYS 139 R CYS 139 1_555 ZA FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc18 O ND1 HIS 141 R HIS 141 1_555 ZA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc19 O SG CYS 158 R CYS 158 1_555 ZA FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc20 O ND1 HIS 161 R HIS 161 1_555 ZA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? # _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 485 n n CHA C4D HEM doub 486 n n CHA HHA HEM sing 487 n n CHB C4A HEM sing 488 n n CHB C1B HEM doub 489 n n CHB HHB HEM sing 490 n n CHC C4B HEM sing 491 n n CHC C1C HEM doub 492 n n CHC HHC HEM sing 493 n n CHD C4C HEM doub 494 n n CHD C1D HEM sing 495 n n CHD HHD HEM sing 496 n n C1A C2A HEM doub 497 n y C1A NA HEM sing 498 n y C2A C3A HEM sing 499 n y C2A CAA HEM sing 500 n n C3A C4A HEM doub 501 n y C3A CMA HEM sing 502 n n C4A NA HEM sing 503 n y CMA HMA HEM sing 504 n n CMA HMAA HEM sing 505 n n CMA HMAB HEM sing 506 n n CAA CBA HEM sing 507 n n CAA HAA HEM sing 508 n n CAA HAAA HEM sing 509 n n CBA CGA HEM sing 510 n n CBA HBA HEM sing 511 n n CBA HBAA HEM sing 512 n n CGA O1A HEM doub 513 n n CGA O2A HEM sing 514 n n C1B C2B HEM sing 515 n n C1B NB HEM sing 516 n n C2B C3B HEM doub 517 n n C2B CMB HEM sing 518 n n C3B C4B HEM sing 519 n n C3B CAB HEM sing 520 n n C4B NB HEM doub 521 n n CMB HMB HEM sing 522 n n CMB HMBA HEM sing 523 n n CMB HMBB HEM sing 524 n n CAB CBB HEM doub 525 n n CAB HAB HEM sing 526 n n CBB HBB HEM sing 527 n n CBB HBBA HEM sing 528 n n C1C C2C HEM sing 529 n y C1C NC HEM sing 530 n y C2C C3C HEM doub 531 n y C2C CMC HEM sing 532 n n C3C C4C HEM sing 533 n y C3C CAC HEM sing 534 n n C4C NC HEM sing 535 n y CMC HMC HEM sing 536 n n CMC HMCA HEM sing 537 n n CMC HMCB HEM sing 538 n n CAC CBC HEM doub 539 n n CAC HAC HEM sing 540 n n CBC HBC HEM sing 541 n n CBC HBCA HEM sing 542 n n C1D C2D HEM sing 543 n n C1D ND HEM doub 544 n n C2D C3D HEM doub 545 n n C2D CMD HEM sing 546 n n C3D C4D HEM sing 547 n n C3D CAD HEM sing 548 n n C4D ND HEM sing 549 n n CMD HMD HEM sing 550 n n CMD HMDA HEM sing 551 n n CMD HMDB HEM sing 552 n n CAD CBD HEM sing 553 n n CAD HAD HEM sing 554 n n CAD HADA HEM sing 555 n n CBD CGD HEM sing 556 n n CBD HBD HEM sing 557 n n CBD HBDA HEM sing 558 n n CGD O1D HEM doub 559 n n CGD O2D HEM sing 560 n n O2A H2A HEM sing 561 n n O2D H2D HEM sing 562 n n FE NA HEM sing 563 n n FE NB HEM sing 564 n n FE NC HEM sing 565 n n FE ND HEM sing 566 n n # _atom_sites.entry_id 3H1J _atom_sites.fract_transf_matrix[1][1] 0.005765 _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] 0.005481 _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] 0.004144 _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 11 UNL A 1 3016 3016 UNL UNL . V 12 HEM C 1 501 501 HEM HEM . W 12 HEM C 1 502 502 HEM HEM . X 13 SMA C 1 2001 2001 SMA SMA . Y 14 UQ C 1 2002 2002 UQ UQ . Z 15 PEE C 1 2007 2007 PEE PEE . AA 15 PEE C 1 2008 2008 PEE PEE . BA 11 UNL C 1 2010 2010 UNL UNL . CA 16 GOL C 1 2011 2011 GOL GOL . DA 11 UNL C 1 2104 2104 UNL UNL . EA 11 UNL C 1 3015 3015 UNL UNL . FA 17 HEC D 1 501 501 HEC HEC . GA 18 CDL D 1 2003 2003 CDL CDL . HA 19 FES E 1 501 501 FES FES . IA 15 PEE E 1 2005 2005 PEE PEE . JA 20 PLC E 1 2009 2009 PLC PLC . KA 11 UNL E 1 2105 2105 UNL UNL . LA 11 UNL E 1 3103 3103 UNL UNL . MA 18 CDL G 1 2004 2004 CDL CDL . NA 15 PEE N 1 3008 3008 PEE PEE . OA 12 HEM P 1 501 501 HEM HEM . PA 12 HEM P 1 502 502 HEM HEM . QA 11 UNL P 1 2015 2015 UNL UNL . RA 13 SMA P 1 3001 3001 SMA SMA . SA 14 UQ P 1 3002 3002 UQ UQ . TA 18 CDL P 1 3004 3004 CDL CDL . UA 15 PEE P 1 3007 3007 PEE PEE . VA 11 UNL P 1 3010 3010 UNL UNL . WA 16 GOL P 1 3011 3011 GOL GOL . XA 11 UNL P 1 3104 3104 UNL UNL . YA 17 HEC Q 1 501 501 HEC HEC . ZA 19 FES R 1 501 501 FES FES . AB 11 UNL R 1 2103 2103 UNL UNL . BB 15 PEE R 1 3005 3005 PEE PEE . CB 20 PLC R 1 3009 3009 PLC PLC . DB 18 CDL S 1 3003 3003 CDL CDL . EB 21 HOH B 1 1234 1234 HOH HOH . FB 21 HOH C 1 381 2 HOH HOH . FB 21 HOH C 2 382 108 HOH HOH . FB 21 HOH C 3 383 119 HOH HOH . FB 21 HOH C 4 384 168 HOH HOH . FB 21 HOH C 5 385 222 HOH HOH . FB 21 HOH C 6 1008 1008 HOH HOH . GB 21 HOH P 1 381 1 HOH HOH . GB 21 HOH P 2 382 28 HOH HOH . GB 21 HOH P 3 383 35 HOH HOH . GB 21 HOH P 4 384 109 HOH HOH . GB 21 HOH P 5 385 214 HOH HOH . GB 21 HOH P 6 959 959 HOH HOH . HB 21 HOH U 1 1233 1233 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 . . . V 12 21.125 137.327 76.64 1 44.73 ? CHA HEM 501 C 1 HETATM 2 C CHB HEM . . . V 12 20.325 132.627 76.412 1 48.37 ? CHB HEM 501 C 1 HETATM 3 C CHC HEM . . . V 12 24.86 131.867 77.694 1 50.18 ? CHC HEM 501 C 1 HETATM 4 C CHD HEM . . . V 12 25.496 136.548 78.257 1 46.15 ? CHD HEM 501 C 1 HETATM 5 C C1A HEM . . . V 12 20.55 136.135 76.493 1 44.95 ? C1A HEM 501 C 1 HETATM 6 C C2A HEM . . . V 12 19.184 135.985 76.128 1 46.41 ? C2A HEM 501 C 1 HETATM 7 C C3A HEM . . . V 12 18.946 134.644 76.059 1 47.82 ? C3A HEM 501 C 1 HETATM 8 C C4A HEM . . . V 12 20.175 134.009 76.426 1 47.24 ? C4A HEM 501 C 1 HETATM 9 C CMA HEM . . . V 12 17.682 133.928 75.534 1 48.33 ? CMA HEM 501 C 1 HETATM 10 C CAA HEM . . . V 12 18.269 137.103 75.667 1 45.53 ? CAA HEM 501 C 1 HETATM 11 C CBA HEM . . . V 12 18.583 137.245 74.193 1 47.88 ? CBA HEM 501 C 1 HETATM 12 C CGA HEM . . . V 12 17.905 138.432 73.557 1 50.1 ? CGA HEM 501 C 1 HETATM 13 O O1A HEM . . . V 12 18.411 139.574 73.707 1 48.67 ? O1A HEM 501 C 1 HETATM 14 O O2A HEM . . . V 12 16.854 138.208 72.91 1 53.14 ? O2A HEM 501 C 1 HETATM 15 C C1B HEM . . . V 12 21.497 131.969 76.731 1 49.15 ? C1B HEM 501 C 1 HETATM 16 C C2B HEM . . . V 12 21.613 130.502 76.867 1 48.68 ? C2B HEM 501 C 1 HETATM 17 C C3B HEM . . . V 12 22.934 130.296 77.155 1 48.98 ? C3B HEM 501 C 1 HETATM 18 C C4B HEM . . . V 12 23.576 131.628 77.286 1 48.4 ? C4B HEM 501 C 1 HETATM 19 C CMB HEM . . . V 12 20.528 129.435 76.731 1 45.28 ? CMB HEM 501 C 1 HETATM 20 C CAB HEM . . . V 12 23.521 129.057 77.294 1 47.25 ? CAB HEM 501 C 1 HETATM 21 C CBB HEM . . . V 12 23.04 128.163 78.369 1 48.9 ? CBB HEM 501 C 1 HETATM 22 C C1C HEM . . . V 12 25.419 133.09 78.062 1 49.49 ? C1C HEM 501 C 1 HETATM 23 C C2C HEM . . . V 12 26.689 133.237 78.755 1 49.39 ? C2C HEM 501 C 1 HETATM 24 C C3C HEM . . . V 12 26.92 134.583 78.805 1 48.73 ? C3C HEM 501 C 1 HETATM 25 C C4C HEM . . . V 12 25.712 135.211 78.286 1 47.68 ? C4C HEM 501 C 1 HETATM 26 C CMC HEM . . . V 12 27.569 132.086 79.271 1 49.36 ? CMC HEM 501 C 1 HETATM 27 C CAC HEM . . . V 12 28.078 135.261 79.215 1 48.84 ? CAC HEM 501 C 1 HETATM 28 C CBC HEM . . . V 12 28.919 134.887 80.429 1 48.51 ? CBC HEM 501 C 1 HETATM 29 C C1D HEM . . . V 12 24.371 137.156 77.905 1 46.19 ? C1D HEM 501 C 1 HETATM 30 C C2D HEM . . . V 12 24.208 138.609 77.801 1 47.44 ? C2D HEM 501 C 1 HETATM 31 C C3D HEM . . . V 12 22.908 138.832 77.403 1 48.54 ? C3D HEM 501 C 1 HETATM 32 C C4D HEM . . . V 12 22.362 137.503 77.126 1 47.44 ? C4D HEM 501 C 1 HETATM 33 C CMD HEM . . . V 12 25.229 139.697 77.986 1 46.73 ? CMD HEM 501 C 1 HETATM 34 C CAD HEM . . . V 12 22.142 140.158 77.418 1 47.78 ? CAD HEM 501 C 1 HETATM 35 C CBD HEM . . . V 12 22.242 141.046 76.205 1 48.46 ? CBD HEM 501 C 1 HETATM 36 C CGD HEM . . . V 12 21.547 140.458 75.016 1 49.23 ? CGD HEM 501 C 1 HETATM 37 O O1D HEM . . . V 12 20.333 140.217 75.097 1 49.98 ? O1D HEM 501 C 1 HETATM 38 O O2D HEM . . . V 12 22.21 140.234 73.991 1 51.54 ? O2D HEM 501 C 1 HETATM 39 N NA HEM . . . V 12 21.163 134.942 76.719 1 45.84 ? NA HEM 501 C 1 HETATM 40 N NB HEM . . . V 12 22.685 132.653 77.097 1 47.84 ? NB HEM 501 C 1 HETATM 41 N NC HEM . . . V 12 24.782 134.299 77.903 1 48.2 ? NC HEM 501 C 1 HETATM 42 N ND HEM . . . V 12 23.25 136.48 77.481 1 46.76 ? ND HEM 501 C 1 HETATM 43 FE FE HEM . . . V 12 22.982 134.604 77.305 1 45.49 ? FE HEM 501 C 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #