data_5NMI # _model_server_result.job_id dfp8IeKktc4QO5WHUkIr5w _model_server_result.datetime_utc '2025-02-17 07:53:21' _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":"AA","auth_seq_id":505}' # _entry.id 5NMI # _exptl.entry_id 5NMI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 1464.043 _entity.id 14 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CARDIOLIPIN _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 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 ? 14 AA N N ? 14 BA N N ? 14 EA N N ? 14 HA N N ? 14 MA N N ? 14 NA 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 'C81 H156 O17 P2 -2' _chem_comp.formula_weight 1464.043 _chem_comp.id CDL _chem_comp.mon_nstd_flag . _chem_comp.name CARDIOLIPIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "DIPHOSPHATIDYL GLYCEROL;BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL" # _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 C1 CDL . . . AA 14 56.126 18.699 -0.437 1 75.1 ? C1 CDL 505 C 1 HETATM 2 O O1 CDL . . . AA 14 54.859 18.778 -1.113 1 54.73 ? O1 CDL 505 C 1 HETATM 3 C CA2 CDL . . . AA 14 56.265 19.97 0.399 1 73.04 ? CA2 CDL 505 C 1 HETATM 4 O OA2 CDL . . . AA 14 57 20.909 -0.373 1 83.92 ? OA2 CDL 505 C 1 HETATM 5 P PA1 CDL . . . AA 14 58.146 21.832 0.274 1 96.05 ? PA1 CDL 505 C 1 HETATM 6 O OA3 CDL . . . AA 14 58.512 21.321 1.645 1 90.62 ? OA3 CDL 505 C 1 HETATM 7 O OA4 CDL . . . AA 14 59.213 22.009 -0.773 1 67.3 ? OA4 CDL 505 C 1 HETATM 8 O OA5 CDL . . . AA 14 57.39 23.233 0.46 1 106.68 ? OA5 CDL 505 C 1 HETATM 9 C CA3 CDL . . . AA 14 56.151 23.286 1.157 1 121.29 ? CA3 CDL 505 C 1 HETATM 10 C CA4 CDL . . . AA 14 55.681 24.747 1.257 1 129.71 ? CA4 CDL 505 C 1 HETATM 11 O OA6 CDL . . . AA 14 55.194 25.018 2.575 1 130.11 ? OA6 CDL 505 C 1 HETATM 12 C CA5 CDL . . . AA 14 54.086 24.195 3.053 1 109.94 ? CA5 CDL 505 C 1 HETATM 13 O OA7 CDL . . . AA 14 53.052 24.075 2.401 1 81.36 ? OA7 CDL 505 C 1 HETATM 14 C C11 CDL . . . AA 14 54.267 23.502 4.374 1 98.88 ? C11 CDL 505 C 1 HETATM 15 C CA6 CDL . . . AA 14 54.602 25.129 0.216 1 130.56 ? CA6 CDL 505 C 1 HETATM 16 O OA8 CDL . . . AA 14 54.982 26.182 -0.656 1 122.26 ? OA8 CDL 505 C 1 HETATM 17 C CA7 CDL . . . AA 14 54.017 27.132 -1.221 1 101.77 ? CA7 CDL 505 C 1 HETATM 18 O OA9 CDL . . . AA 14 52.83 27.031 -0.983 1 98.08 ? OA9 CDL 505 C 1 HETATM 19 C C31 CDL . . . AA 14 54.521 28.256 -2.096 1 77.45 ? C31 CDL 505 C 1 HETATM 20 C C32 CDL . . . AA 14 55.988 28.541 -1.779 1 73.51 ? C32 CDL 505 C 1 HETATM 21 C C33 CDL . . . AA 14 56.253 28.795 -0.291 1 66.07 ? C33 CDL 505 C 1 HETATM 22 C C34 CDL . . . AA 14 57.736 29.017 -0.057 1 65.17 ? C34 CDL 505 C 1 HETATM 23 C C35 CDL . . . AA 14 58.064 30.501 -0.145 1 60.52 ? C35 CDL 505 C 1 HETATM 24 C C36 CDL . . . AA 14 59.563 30.741 -0.02 1 53.69 ? C36 CDL 505 C 1 HETATM 25 C C37 CDL . . . AA 14 60.243 30.648 -1.379 1 45.94 ? C37 CDL 505 C 1 HETATM 26 C CB2 CDL . . . AA 14 56.217 17.422 0.416 1 90.35 ? CB2 CDL 505 C 1 HETATM 27 O OB2 CDL . . . AA 14 56.851 16.335 -0.276 1 93.77 ? OB2 CDL 505 C 1 HETATM 28 P PB2 CDL . . . AA 14 57.366 15.016 0.504 1 71.02 ? PB2 CDL 505 C 1 HETATM 29 O OB3 CDL . . . AA 14 58.856 14.938 0.347 1 54.87 ? OB3 CDL 505 C 1 HETATM 30 O OB4 CDL . . . AA 14 56.76 14.962 1.887 1 74.36 ? OB4 CDL 505 C 1 HETATM 31 O OB5 CDL . . . AA 14 56.744 13.83 -0.373 1 75.46 ? OB5 CDL 505 C 1 HETATM 32 C CB3 CDL . . . AA 14 55.339 13.76 -0.487 1 82.46 ? CB3 CDL 505 C 1 HETATM 33 C CB4 CDL . . . AA 14 55.019 12.983 -1.743 1 92.95 ? CB4 CDL 505 C 1 HETATM 34 O OB6 CDL . . . AA 14 54.939 13.839 -2.879 1 89.45 ? OB6 CDL 505 C 1 HETATM 35 C CB5 CDL . . . AA 14 55.426 13.095 -4.018 1 102.99 ? CB5 CDL 505 C 1 HETATM 36 O OB7 CDL . . . AA 14 56.617 12.869 -4.06 1 122.14 ? OB7 CDL 505 C 1 HETATM 37 C C51 CDL . . . AA 14 54.48 12.592 -5.081 1 88.71 ? C51 CDL 505 C 1 HETATM 38 C CB6 CDL . . . AA 14 53.702 12.239 -1.65 1 98.26 ? CB6 CDL 505 C 1 HETATM 39 O OB8 CDL . . . AA 14 53.976 10.896 -1.293 1 99.09 ? OB8 CDL 505 C 1 HETATM 40 C CB7 CDL . . . AA 14 52.922 10.139 -0.648 1 88.22 ? CB7 CDL 505 C 1 HETATM 41 O OB9 CDL . . . AA 14 53.007 9.893 0.542 1 78.84 ? OB9 CDL 505 C 1 HETATM 42 C C71 CDL . . . AA 14 51.731 9.681 -1.449 1 84.33 ? C71 CDL 505 C 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 70 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 42 #