data_5NMI # _model_server_result.job_id kRZ-KEmUq41MILRbq2bV1Q _model_server_result.datetime_utc '2024-11-09 02:34:15' _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 5nmi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"OA","auth_seq_id":501}' # _entry.id 5NMI # _exptl.entry_id 5NMI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 15 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 5NMI _cell.length_a 129.477 _cell.length_b 129.477 _cell.length_c 720.294 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NMI _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 22-meric _pdbx_struct_assembly.oligomeric_count 22 _pdbx_struct_assembly.details 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 _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 ? 15 CA N N ? 15 OA 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 222 E CYS 144 1_555 E SG CYS 238 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 H SG CYS 37 H CYS 24 1_555 H SG CYS 81 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 H SG CYS 53 H CYS 40 1_555 H SG CYS 67 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 S SG CYS 37 U CYS 24 1_555 S SG CYS 81 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 S SG CYS 53 U CYS 40 1_555 S SG CYS 67 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 C NE2 HIS 76 C HIS 83 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc2 C NE2 HIS 90 C HIS 97 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? metalc ? metalc3 C NE2 HIS 175 C HIS 182 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? metalc ? metalc4 C NE2 HIS 189 C HIS 196 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? covale ? covale1 D SG CYS 36 D CYS 37 1_555 CA CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? covale ? covale2 D SG CYS 39 D CYS 40 1_555 CA CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.665 ? metalc ? metalc5 D NE2 HIS 40 D HIS 41 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? metalc ? metalc6 D SD MET 159 D MET 160 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc7 E SG CYS 217 E CYS 139 1_555 FA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc8 E ND1 HIS 219 E HIS 141 1_555 FA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc9 E SG CYS 236 E CYS 158 1_555 FA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc10 E ND1 HIS 239 E HIS 161 1_555 FA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc11 N NE2 HIS 76 P HIS 83 1_555 IA FE HEM . P HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? metalc ? metalc12 N NE2 HIS 90 P HIS 97 1_555 JA FE HEM . P HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc13 N NE2 HIS 175 P HIS 182 1_555 IA FE HEM . P HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? metalc ? metalc14 N NE2 HIS 189 P HIS 196 1_555 JA FE HEM . P HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? covale ? covale3 O SG CYS 36 Q CYS 37 1_555 OA CAB HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.626 ? covale ? covale4 O SG CYS 39 Q CYS 40 1_555 OA CAC HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.678 ? metalc ? metalc15 O NE2 HIS 40 Q HIS 41 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc16 O SD MET 159 Q MET 160 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5NMI _atom_sites.fract_transf_matrix[1][1] 0.007723 _atom_sites.fract_transf_matrix[1][2] 0.004459 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008918 _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] 0.001388 _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 W 11 HEM C 1 501 501 HEM HEM . X 11 HEM C 1 502 502 HEM HEM . Y 12 MJM C 1 503 503 MJM MJM . Z 13 PEE C 1 504 504 PEE PEE . AA 14 CDL C 1 505 505 CDL CDL . BA 14 CDL C 1 506 501 CDL CDL . CA 15 HEC D 1 501 501 HEC HEC . DA 13 PEE D 1 502 502 PEE PEE . EA 14 CDL D 1 503 503 CDL CDL . FA 16 FES E 1 501 501 FES FES . GA 13 PEE E 1 502 502 PEE PEE . HA 14 CDL P 1 401 503 CDL CDL . IA 11 HEM P 1 402 501 HEM HEM . JA 11 HEM P 1 403 502 HEM HEM . KA 12 MJM P 1 404 503 MJM MJM . LA 13 PEE P 1 405 504 PEE PEE . MA 14 CDL P 1 406 505 CDL CDL . NA 14 CDL P 1 407 501 CDL CDL . OA 15 HEC Q 1 501 501 HEC HEC . PA 13 PEE R 1 201 502 PEE PEE . QA 13 PEE R 1 202 502 PEE PEE . # 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 FE FE HEC . . . OA 15 13.795 20.397 -60.292 1 76.19 ? FE HEC 501 Q 1 HETATM 2 C CHA HEC . . . OA 15 17.229 20.442 -59.76 1 60.54 ? CHA HEC 501 Q 1 HETATM 3 C CHB HEC . . . OA 15 13.512 23.26 -58.458 1 86.02 ? CHB HEC 501 Q 1 HETATM 4 C CHC HEC . . . OA 15 10.428 20.481 -60.992 1 92.5 ? CHC HEC 501 Q 1 HETATM 5 C CHD HEC . . . OA 15 14.089 17.417 -61.939 1 69.22 ? CHD HEC 501 Q 1 HETATM 6 N NA HEC . . . OA 15 15.128 21.631 -59.286 1 77.29 ? NA HEC 501 Q 1 HETATM 7 C C1A HEC . . . OA 15 16.446 21.514 -59.177 1 74.58 ? C1A HEC 501 Q 1 HETATM 8 C C2A HEC . . . OA 15 17.095 22.554 -58.389 1 76.25 ? C2A HEC 501 Q 1 HETATM 9 C C3A HEC . . . OA 15 16.002 23.4 -57.977 1 78.24 ? C3A HEC 501 Q 1 HETATM 10 C C4A HEC . . . OA 15 14.852 22.728 -58.602 1 79.29 ? C4A HEC 501 Q 1 HETATM 11 C CMA HEC . . . OA 15 16.087 24.644 -57.152 1 80.69 ? CMA HEC 501 Q 1 HETATM 12 C CAA HEC . . . OA 15 18.516 22.687 -58.006 1 75.39 ? CAA HEC 501 Q 1 HETATM 13 C CBA HEC . . . OA 15 19.349 23.547 -58.905 1 80.29 ? CBA HEC 501 Q 1 HETATM 14 C CGA HEC . . . OA 15 20.714 23.58 -58.243 1 94.52 ? CGA HEC 501 Q 1 HETATM 15 O O1A HEC . . . OA 15 21.275 22.503 -57.931 1 94.55 ? O1A HEC 501 Q 1 HETATM 16 O O2A HEC . . . OA 15 21.254 24.678 -58.01 1 107.82 ? O2A HEC 501 Q 1 HETATM 17 N NB HEC . . . OA 15 12.218 21.661 -59.809 1 82.2 ? NB HEC 501 Q 1 HETATM 18 C C1B HEC . . . OA 15 12.282 22.746 -59.052 1 95.79 ? C1B HEC 501 Q 1 HETATM 19 C C2B HEC . . . OA 15 11.027 23.482 -58.872 1 99.78 ? C2B HEC 501 Q 1 HETATM 20 C C3B HEC . . . OA 15 10.111 22.622 -59.631 1 94.18 ? C3B HEC 501 Q 1 HETATM 21 C C4B HEC . . . OA 15 10.953 21.563 -60.176 1 83.99 ? C4B HEC 501 Q 1 HETATM 22 C CMB HEC . . . OA 15 10.798 24.731 -58.077 1 93.1 ? CMB HEC 501 Q 1 HETATM 23 C CAB HEC . . . OA 15 8.661 22.733 -59.861 1 130.5 ? CAB HEC 501 Q 1 HETATM 24 C CBB HEC . . . OA 15 7.835 23.865 -59.336 1 145.14 ? CBB HEC 501 Q 1 HETATM 25 N NC HEC . . . OA 15 12.472 19.154 -61.312 1 85.21 ? NC HEC 501 Q 1 HETATM 26 C C1C HEC . . . OA 15 11.166 19.334 -61.494 1 102.2 ? C1C HEC 501 Q 1 HETATM 27 C C2C HEC . . . OA 15 10.456 18.281 -62.232 1 111.64 ? C2C HEC 501 Q 1 HETATM 28 C C3C HEC . . . OA 15 11.537 17.345 -62.529 1 92.93 ? C3C HEC 501 Q 1 HETATM 29 C C4C HEC . . . OA 15 12.741 17.996 -61.907 1 73.62 ? C4C HEC 501 Q 1 HETATM 30 C CMC HEC . . . OA 15 9.012 18.196 -62.593 1 130.04 ? CMC HEC 501 Q 1 HETATM 31 C CAC HEC . . . OA 15 11.452 15.999 -63.203 1 100.97 ? CAC HEC 501 Q 1 HETATM 32 C CBC HEC . . . OA 15 10.308 15.311 -63.956 1 100.13 ? CBC HEC 501 Q 1 HETATM 33 N ND HEC . . . OA 15 15.382 19.15 -60.774 1 64.04 ? ND HEC 501 Q 1 HETATM 34 C C1D HEC . . . OA 15 15.323 18.004 -61.427 1 67.93 ? C1D HEC 501 Q 1 HETATM 35 C C2D HEC . . . OA 15 16.626 17.34 -61.612 1 67.65 ? C2D HEC 501 Q 1 HETATM 36 C C3D HEC . . . OA 15 17.566 18.242 -60.965 1 62.66 ? C3D HEC 501 Q 1 HETATM 37 C C4D HEC . . . OA 15 16.682 19.316 -60.498 1 59 ? C4D HEC 501 Q 1 HETATM 38 C CMD HEC . . . OA 15 16.946 16.063 -62.31 1 64.63 ? CMD HEC 501 Q 1 HETATM 39 C CAD HEC . . . OA 15 19.057 18.116 -60.847 1 66.99 ? CAD HEC 501 Q 1 HETATM 40 C CBD HEC . . . OA 15 19.63 19.024 -61.931 1 63.34 ? CBD HEC 501 Q 1 HETATM 41 C CGD HEC . . . OA 15 21.139 18.969 -61.984 1 64.87 ? CGD HEC 501 Q 1 HETATM 42 O O1D HEC . . . OA 15 21.674 18.924 -63.116 1 70.5 ? O1D HEC 501 Q 1 HETATM 43 O O2D HEC . . . OA 15 21.792 18.984 -60.915 1 72.17 ? O2D HEC 501 Q 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 57 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #