data_5NMI # _model_server_result.job_id SYp0jig87jLdAeAaWxnd8g _model_server_result.datetime_utc '2024-11-23 12:32:22' _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":"HA","auth_seq_id":401}' # _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 . . . HA 14 31.077 59.307 -23.786 1 134.15 ? C1 CDL 401 P 1 HETATM 2 O O1 CDL . . . HA 14 30.381 58.238 -24.443 1 117.43 ? O1 CDL 401 P 1 HETATM 3 C CA2 CDL . . . HA 14 30.597 60.63 -24.368 1 150.89 ? CA2 CDL 401 P 1 HETATM 4 O OA2 CDL . . . HA 14 31.026 61.719 -23.564 1 159.72 ? OA2 CDL 401 P 1 HETATM 5 P PA1 CDL . . . HA 14 30.743 63.225 -24.048 1 141.89 ? PA1 CDL 401 P 1 HETATM 6 O OA3 CDL . . . HA 14 32.05 63.8 -24.525 1 110.4 ? OA3 CDL 401 P 1 HETATM 7 O OA4 CDL . . . HA 14 29.537 63.24 -24.96 1 135.36 ? OA4 CDL 401 P 1 HETATM 8 O OA5 CDL . . . HA 14 30.355 63.932 -22.66 1 121.06 ? OA5 CDL 401 P 1 HETATM 9 C CA3 CDL . . . HA 14 29.278 64.859 -22.595 1 85.83 ? CA3 CDL 401 P 1 HETATM 10 C CB2 CDL . . . HA 14 30.826 59.261 -22.281 1 117.71 ? CB2 CDL 401 P 1 HETATM 11 O OB2 CDL . . . HA 14 30.671 57.908 -21.908 1 127.12 ? OB2 CDL 401 P 1 HETATM 12 P PB2 CDL . . . HA 14 29.225 57.218 -21.86 1 113.27 ? PB2 CDL 401 P 1 HETATM 13 O OB3 CDL . . . HA 14 28.996 56.936 -20.405 1 109.69 ? OB3 CDL 401 P 1 HETATM 14 O OB4 CDL . . . HA 14 28.216 58.033 -22.617 1 128.21 ? OB4 CDL 401 P 1 HETATM 15 O OB5 CDL . . . HA 14 29.498 55.897 -22.74 1 109.23 ? OB5 CDL 401 P 1 HETATM 16 C CB3 CDL . . . HA 14 29.586 54.611 -22.122 1 108.12 ? CB3 CDL 401 P 1 HETATM 17 C CB4 CDL . . . HA 14 29.165 53.582 -23.145 1 110.12 ? CB4 CDL 401 P 1 HETATM 18 O OB6 CDL . . . HA 14 27.877 53.976 -23.624 1 104.74 ? OB6 CDL 401 P 1 HETATM 19 C CB5 CDL . . . HA 14 27.756 54.172 -25.053 1 96.13 ? CB5 CDL 401 P 1 HETATM 20 O OB7 CDL . . . HA 14 26.66 53.951 -25.553 1 95.8 ? OB7 CDL 401 P 1 HETATM 21 C C51 CDL . . . HA 14 28.911 54.651 -25.907 1 90.82 ? C51 CDL 401 P 1 HETATM 22 C C52 CDL . . . HA 14 28.71 54.351 -27.392 1 87.44 ? C52 CDL 401 P 1 HETATM 23 C C53 CDL . . . HA 14 29.015 52.888 -27.686 1 88.78 ? C53 CDL 401 P 1 HETATM 24 C C54 CDL . . . HA 14 28.021 52.266 -28.647 1 83.37 ? C54 CDL 401 P 1 HETATM 25 C C55 CDL . . . HA 14 28.354 50.789 -28.797 1 75.93 ? C55 CDL 401 P 1 HETATM 26 C C56 CDL . . . HA 14 27.692 50.191 -30.026 1 70.11 ? C56 CDL 401 P 1 HETATM 27 C C57 CDL . . . HA 14 27.78 48.673 -29.949 1 68.44 ? C57 CDL 401 P 1 HETATM 28 C C58 CDL . . . HA 14 27.048 48.007 -31.099 1 63.83 ? C58 CDL 401 P 1 HETATM 29 C C59 CDL . . . HA 14 25.536 48.058 -30.892 1 68.84 ? C59 CDL 401 P 1 HETATM 30 C C60 CDL . . . HA 14 24.81 46.923 -31.607 1 72.5 ? C60 CDL 401 P 1 HETATM 31 C C61 CDL . . . HA 14 24.254 47.329 -32.97 1 72.81 ? C61 CDL 401 P 1 HETATM 32 C C62 CDL . . . HA 14 25.318 47.249 -34.059 1 72.42 ? C62 CDL 401 P 1 HETATM 33 C CB6 CDL . . . HA 14 29.068 52.158 -22.638 1 99.65 ? CB6 CDL 401 P 1 HETATM 34 O OB8 CDL . . . HA 14 29.171 51.352 -23.811 1 94.34 ? OB8 CDL 401 P 1 HETATM 35 C CB7 CDL . . . HA 14 29.411 49.916 -23.83 1 85.25 ? CB7 CDL 401 P 1 HETATM 36 O OB9 CDL . . . HA 14 29.469 49.286 -22.786 1 90.79 ? OB9 CDL 401 P 1 HETATM 37 C C71 CDL . . . HA 14 29.587 49.269 -25.185 1 72.28 ? C71 CDL 401 P 1 HETATM 38 C C72 CDL . . . HA 14 29.727 47.757 -25.091 1 56.41 ? C72 CDL 401 P 1 HETATM 39 C C73 CDL . . . HA 14 29.862 47.165 -26.488 1 57.32 ? C73 CDL 401 P 1 HETATM 40 C C74 CDL . . . HA 14 28.918 45.99 -26.703 1 58.72 ? C74 CDL 401 P 1 HETATM 41 C C75 CDL . . . HA 14 28.658 45.74 -28.183 1 58.39 ? C75 CDL 401 P 1 HETATM 42 C C76 CDL . . . HA 14 28.684 44.251 -28.508 1 53.3 ? C76 CDL 401 P 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 42 #