data_5NMI # _model_server_result.job_id dFy8o3wHfPzRkuF0UYRSMg _model_server_result.datetime_utc '2024-11-23 11:50:47' _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":"W","auth_seq_id":501}' # _entry.id 5NMI # _exptl.entry_id 5NMI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 11 _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 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 ? 11 W N N ? 11 X N N ? 11 IA N N ? 11 JA 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 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 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 C CHA HEM . . . W 11 24.352 5.497 -17.724 1 60.09 ? CHA HEM 501 C 1 HETATM 2 C CHB HEM . . . W 11 24.83 6.896 -13.121 1 63.35 ? CHB HEM 501 C 1 HETATM 3 C CHC HEM . . . W 11 27.702 10.514 -14.552 1 57.96 ? CHC HEM 501 C 1 HETATM 4 C CHD HEM . . . W 11 27.063 9.24 -19.173 1 54.77 ? CHD HEM 501 C 1 HETATM 5 C C1A HEM . . . W 11 24.249 5.553 -16.358 1 62.12 ? C1A HEM 501 C 1 HETATM 6 C C2A HEM . . . W 11 23.559 4.602 -15.56 1 61.97 ? C2A HEM 501 C 1 HETATM 7 C C3A HEM . . . W 11 23.691 5.003 -14.259 1 54.42 ? C3A HEM 501 C 1 HETATM 8 C C4A HEM . . . W 11 24.464 6.194 -14.263 1 58.01 ? C4A HEM 501 C 1 HETATM 9 C CMA HEM . . . W 11 23.138 4.314 -13.021 1 54.13 ? CMA HEM 501 C 1 HETATM 10 C CAA HEM . . . W 11 22.854 3.349 -16.064 1 70.53 ? CAA HEM 501 C 1 HETATM 11 C CBA HEM . . . W 11 23.923 2.24 -16.176 1 86.51 ? CBA HEM 501 C 1 HETATM 12 C CGA HEM . . . W 11 23.389 0.973 -16.78 1 90.19 ? CGA HEM 501 C 1 HETATM 13 O O1A HEM . . . W 11 22.852 0.107 -16.057 1 78.18 ? O1A HEM 501 C 1 HETATM 14 O O2A HEM . . . W 11 23.508 0.783 -18.004 1 77.02 ? O2A HEM 501 C 1 HETATM 15 C C1B HEM . . . W 11 25.683 8.014 -13.092 1 63.21 ? C1B HEM 501 C 1 HETATM 16 C C2B HEM . . . W 11 26.07 8.712 -11.898 1 62.54 ? C2B HEM 501 C 1 HETATM 17 C C3B HEM . . . W 11 26.9 9.737 -12.291 1 59.03 ? C3B HEM 501 C 1 HETATM 18 C C4B HEM . . . W 11 26.971 9.63 -13.772 1 55.95 ? C4B HEM 501 C 1 HETATM 19 C CMB HEM . . . W 11 25.666 8.361 -10.484 1 64.57 ? CMB HEM 501 C 1 HETATM 20 C CAB HEM . . . W 11 27.548 10.828 -11.515 1 63.21 ? CAB HEM 501 C 1 HETATM 21 C CBB HEM . . . W 11 27.218 11.186 -10.281 1 69.74 ? CBB HEM 501 C 1 HETATM 22 C C1C HEM . . . W 11 27.779 10.498 -15.934 1 59 ? C1C HEM 501 C 1 HETATM 23 C C2C HEM . . . W 11 28.439 11.464 -16.678 1 64.24 ? C2C HEM 501 C 1 HETATM 24 C C3C HEM . . . W 11 28.247 11.14 -18.017 1 55.09 ? C3C HEM 501 C 1 HETATM 25 C C4C HEM . . . W 11 27.49 9.919 -18.058 1 52.88 ? C4C HEM 501 C 1 HETATM 26 C CMC HEM . . . W 11 29.174 12.648 -16.082 1 66.74 ? CMC HEM 501 C 1 HETATM 27 C CAC HEM . . . W 11 28.828 11.847 -19.14 1 51.46 ? CAC HEM 501 C 1 HETATM 28 C CBC HEM . . . W 11 29.681 12.871 -19.006 1 52.53 ? CBC HEM 501 C 1 HETATM 29 C C1D HEM . . . W 11 26.26 8.098 -19.11 1 57.55 ? C1D HEM 501 C 1 HETATM 30 C C2D HEM . . . W 11 25.874 7.383 -20.343 1 62.11 ? C2D HEM 501 C 1 HETATM 31 C C3D HEM . . . W 11 25.129 6.341 -19.948 1 58.85 ? C3D HEM 501 C 1 HETATM 32 C C4D HEM . . . W 11 25.063 6.423 -18.474 1 56.62 ? C4D HEM 501 C 1 HETATM 33 C CMD HEM . . . W 11 26.188 7.686 -21.799 1 62.56 ? CMD HEM 501 C 1 HETATM 34 C CAD HEM . . . W 11 24.482 5.335 -20.887 1 55.73 ? CAD HEM 501 C 1 HETATM 35 C CBD HEM . . . W 11 25.356 4.094 -21.124 1 55.73 ? CBD HEM 501 C 1 HETATM 36 C CGD HEM . . . W 11 25.083 3.036 -20.085 1 60.54 ? CGD HEM 501 C 1 HETATM 37 O O1D HEM . . . W 11 26.051 2.522 -19.481 1 66.92 ? O1D HEM 501 C 1 HETATM 38 O O2D HEM . . . W 11 23.904 2.685 -19.824 1 56.97 ? O2D HEM 501 C 1 HETATM 39 N NA HEM . . . W 11 24.794 6.521 -15.551 1 60.94 ? NA HEM 501 C 1 HETATM 40 N NB HEM . . . W 11 26.233 8.596 -14.162 1 59.32 ? NB HEM 501 C 1 HETATM 41 N NC HEM . . . W 11 27.189 9.601 -16.77 1 53.35 ? NC HEM 501 C 1 HETATM 42 N ND HEM . . . W 11 25.758 7.486 -18.005 1 54.55 ? ND HEM 501 C 1 HETATM 43 FE FE HEM . . . W 11 25.978 8.003 -16.175 1 55.63 ? FE HEM 501 C 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #