data_6YMX # _model_server_result.job_id ncaaLPD2pmysBgcdc0yqVg _model_server_result.datetime_utc '2024-12-27 03:30:40' _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 6ymx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HB","auth_seq_id":401}' # _entry.id 6YMX # _exptl.entry_id 6YMX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 616.487 _entity.id 34 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 6 _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 6YMX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YMX _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 PISA _pdbx_struct_assembly.oligomeric_details 32-meric _pdbx_struct_assembly.oligomeric_count 32 _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,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 34 WA N N ? 34 XA N N ? 34 CB N N ? 34 HB N N ? 34 IB N N ? 34 OB 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 J SG CYS 22 j CYS 27 1_555 J SG CYS 54 j CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 J SG CYS 32 j CYS 37 1_555 J SG CYS 43 j CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 Q SG CYS 134 E CYS 164 1_555 Q SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 R SG CYS 28 F CYS 101 1_555 R SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 Z SG CYS 134 P CYS 164 1_555 Z SG CYS 150 P CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 AA SG CYS 29 Q CYS 101 1_555 AA SG CYS 51 Q CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 B N ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.287 ? covale ? covale2 B C ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.562 ? covale ? covale3 B CB ILE 46 b ILE 61 1_555 MA C23 PTY . b PTY 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.619 ? covale ? covale4 C CE MET 217 c MET 218 1_555 NA C36 PTY . c PTY 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale5 C CE MET 217 c MET 218 1_555 NA C37 PTY . c PTY 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A NE2 HIS 58 a HIS 62 1_555 HA FE HEA . a HEA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc2 A ND1 HIS 237 a HIS 241 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc3 A NE2 HIS 286 a HIS 290 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 A NE2 HIS 287 a HIS 291 1_555 GA CU CU . a CU 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 A NE2 HIS 374 a HIS 378 1_555 HA FE HEA . a HEA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc6 B O GLU 208 b GLU 223 1_555 LA CU1 CUA . b CUA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc7 B ND1 HIS 214 b HIS 229 1_555 LA CU1 CUA . b CUA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc8 D SG CYS 105 d CYS 134 1_555 PA ZN ZN . d ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc9 O NE2 HIS 82 C HIS 82 1_555 WA FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc10 O NE2 HIS 96 C HIS 96 1_555 XA FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc11 O NE2 HIS 183 C HIS 183 1_555 WA FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc12 O NE2 HIS 197 C HIS 197 1_555 XA FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc13 P NE2 HIS 44 D HIS 105 1_555 CB FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc14 X NE2 HIS 82 N HIS 82 1_555 HB FE HEM . N HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc15 X NE2 HIS 96 N HIS 96 1_555 IB FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc16 X NE2 HIS 183 N HIS 183 1_555 HB FE HEM . N HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc17 X NE2 HIS 197 N HIS 197 1_555 IB FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc18 Y NE2 HIS 44 O HIS 105 1_555 OB FE HEM . O HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? # _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 # _atom_sites.entry_id 6YMX _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 GA 26 CU a 1 601 601 CU CU . HA 27 HEA a 1 602 602 HEA HEA . IA 27 HEA a 1 603 603 HEA HEA . JA 28 PTY a 1 604 7 PTY PTY . KA 29 CN3 a 1 605 1 CN3 CN3 . LA 30 CUA b 1 301 301 CUA CUA . MA 28 PTY b 1 302 1 PTY PTY . NA 28 PTY c 1 301 6 PTY PTY . OA 31 PCF c 1 302 3 PCF PCF . PA 32 ZN d 1 201 1 ZN ZN . QA 31 PCF e 1 201 2 PCF PCF . RA 28 PTY i 1 101 3 PTY PTY . SA 28 PTY m 1 101 4 PTY PTY . TA 28 PTY m 1 102 5 PTY PTY . UA 31 PCF m 1 103 1 PCF PCF . VA 33 6PH C 1 401 401 6PH 6PH . WA 34 HEM C 1 402 402 HEM HEM . XA 34 HEM C 1 403 403 HEM HEM . YA 35 8PE C 1 404 404 8PE 8PE . ZA 36 CN5 C 1 405 405 CN5 CN5 . AB 37 UQ6 C 1 406 406 UQ6 UQ6 . BB 38 9PE C 1 407 401 9PE 9PE . CB 34 HEM D 1 401 401 HEM HEM . DB 28 PTY D 1 402 2 PTY PTY . EB 39 7PH E 1 301 402 7PH 7PH . FB 40 FES E 1 302 301 FES FES . GB 31 PCF I 1 101 101 PCF PCF . HB 34 HEM N 1 401 403 HEM HEM . IB 34 HEM N 1 402 404 HEM HEM . JB 37 UQ6 N 1 403 405 UQ6 UQ6 . KB 35 8PE N 1 404 406 8PE 8PE . LB 38 9PE N 1 405 407 9PE 9PE . MB 29 CN3 N 1 406 408 CN3 CN3 . NB 33 6PH O 1 401 402 6PH 6PH . OB 34 HEM O 1 402 401 HEM HEM . PB 39 7PH O 1 403 301 7PH 7PH . QB 40 FES P 1 301 302 FES FES . RB 31 PCF T 1 101 101 PCF PCF . # 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 . . . HB 34 199.491 230.16 222.474 1 57.76 ? CHA HEM 401 N 1 HETATM 2 C CHB HEM . . . HB 34 201.205 226.201 224.594 1 57.76 ? CHB HEM 401 N 1 HETATM 3 C CHC HEM . . . HB 34 197.458 223.799 222.86 1 57.76 ? CHC HEM 401 N 1 HETATM 4 C CHD HEM . . . HB 34 195.603 227.801 220.995 1 57.76 ? CHD HEM 401 N 1 HETATM 5 C C1A HEM . . . HB 34 200.262 229.302 223.209 1 57.76 ? C1A HEM 401 N 1 HETATM 6 C C2A HEM . . . HB 34 201.459 229.654 223.921 1 57.76 ? C2A HEM 401 N 1 HETATM 7 C C3A HEM . . . HB 34 201.93 228.571 224.504 1 57.76 ? C3A HEM 401 N 1 HETATM 8 C C4A HEM . . . HB 34 201.054 227.487 224.181 1 57.76 ? C4A HEM 401 N 1 HETATM 9 C CMA HEM . . . HB 34 203.197 228.496 225.364 1 57.76 ? CMA HEM 401 N 1 HETATM 10 C CAA HEM . . . HB 34 202.095 231.045 224.012 1 57.76 ? CAA HEM 401 N 1 HETATM 11 C CBA HEM . . . HB 34 201.297 231.889 224.985 1 57.76 ? CBA HEM 401 N 1 HETATM 12 C CGA HEM . . . HB 34 201.994 233.199 225.131 1 57.76 ? CGA HEM 401 N 1 HETATM 13 O O1A HEM . . . HB 34 201.332 234.242 224.937 1 57.76 ? O1A HEM 401 N 1 HETATM 14 O O2A HEM . . . HB 34 203.21 233.192 225.429 1 57.76 ? O2A HEM 401 N 1 HETATM 15 C C1B HEM . . . HB 34 200.339 225.195 224.292 1 57.76 ? C1B HEM 401 N 1 HETATM 16 C C2B HEM . . . HB 34 200.489 223.814 224.677 1 57.76 ? C2B HEM 401 N 1 HETATM 17 C C3B HEM . . . HB 34 199.433 223.153 224.19 1 57.76 ? C3B HEM 401 N 1 HETATM 18 C C4B HEM . . . HB 34 198.621 224.11 223.496 1 57.76 ? C4B HEM 401 N 1 HETATM 19 C CMB HEM . . . HB 34 201.7 223.333 225.504 1 57.76 ? CMB HEM 401 N 1 HETATM 20 C CAB HEM . . . HB 34 198.991 221.676 224.231 1 57.76 ? CAB HEM 401 N 1 HETATM 21 C CBB HEM . . . HB 34 199.672 220.641 224.72 1 57.76 ? CBB HEM 401 N 1 HETATM 22 C C1C HEM . . . HB 34 196.642 224.672 222.205 1 57.76 ? C1C HEM 401 N 1 HETATM 23 C C2C HEM . . . HB 34 195.418 224.312 221.541 1 57.76 ? C2C HEM 401 N 1 HETATM 24 C C3C HEM . . . HB 34 194.896 225.385 221.018 1 57.76 ? C3C HEM 401 N 1 HETATM 25 C C4C HEM . . . HB 34 195.765 226.495 221.341 1 57.76 ? C4C HEM 401 N 1 HETATM 26 C CMC HEM . . . HB 34 194.781 222.924 221.421 1 57.76 ? CMC HEM 401 N 1 HETATM 27 C CAC HEM . . . HB 34 193.571 225.298 220.251 1 57.76 ? CAC HEM 401 N 1 HETATM 28 C CBC HEM . . . HB 34 193.116 226.245 219.44 1 57.76 ? CBC HEM 401 N 1 HETATM 29 C C1D HEM . . . HB 34 196.524 228.772 221.206 1 57.76 ? C1D HEM 401 N 1 HETATM 30 C C2D HEM . . . HB 34 196.416 230.111 220.702 1 57.76 ? C2D HEM 401 N 1 HETATM 31 C C3D HEM . . . HB 34 197.486 230.774 221.107 1 57.76 ? C3D HEM 401 N 1 HETATM 32 C C4D HEM . . . HB 34 198.301 229.862 221.876 1 57.76 ? C4D HEM 401 N 1 HETATM 33 C CMD HEM . . . HB 34 195.244 230.628 219.852 1 57.76 ? CMD HEM 401 N 1 HETATM 34 C CAD HEM . . . HB 34 197.823 232.24 220.809 1 57.76 ? CAD HEM 401 N 1 HETATM 35 C CBD HEM . . . HB 34 197.087 233.156 221.767 1 57.76 ? CBD HEM 401 N 1 HETATM 36 C CGD HEM . . . HB 34 197.874 233.253 223.035 1 57.76 ? CGD HEM 401 N 1 HETATM 37 O O1D HEM . . . HB 34 199.122 233.254 222.959 1 57.76 ? O1D HEM 401 N 1 HETATM 38 O O2D HEM . . . HB 34 197.254 233.348 224.118 1 57.76 ? O2D HEM 401 N 1 HETATM 39 N NA HEM . . . HB 34 200.041 227.961 223.389 1 57.76 ? NA HEM 401 N 1 HETATM 40 N NB HEM . . . HB 34 199.187 225.35 223.573 1 57.76 ? NB HEM 401 N 1 HETATM 41 N NC HEM . . . HB 34 196.837 226.024 222.069 1 57.76 ? NC HEM 401 N 1 HETATM 42 N ND HEM . . . HB 34 197.685 228.637 221.925 1 57.76 ? ND HEM 401 N 1 HETATM 43 FE FE HEM . . . HB 34 198.458 227.018 222.855 1 57.76 ? FE HEM 401 N 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 121 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #