data_5NMI # _model_server_result.job_id BG9ynmgYu8kWKt-rRAvi7A _model_server_result.datetime_utc '2024-11-23 12:47:10' _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":"BA","auth_seq_id":506}' # _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 . . . BA 14 35.626 2.394 14.357 1 88.25 ? C1 CDL 506 C 1 HETATM 2 O O1 CDL . . . BA 14 34.244 2.097 14.161 1 84.22 ? O1 CDL 506 C 1 HETATM 3 C CA2 CDL . . . BA 14 36.382 1.856 13.17 1 71.27 ? CA2 CDL 506 C 1 HETATM 4 O OA2 CDL . . . BA 14 37.757 1.977 13.463 1 60.64 ? OA2 CDL 506 C 1 HETATM 5 P PA1 CDL . . . BA 14 38.804 1.95 12.272 1 69.8 ? PA1 CDL 506 C 1 HETATM 6 O OA3 CDL . . . BA 14 40.172 1.609 12.776 1 67.48 ? OA3 CDL 506 C 1 HETATM 7 O OA4 CDL . . . BA 14 38.568 3.225 11.511 1 85.12 ? OA4 CDL 506 C 1 HETATM 8 O OA5 CDL . . . BA 14 38.304 0.676 11.442 1 73.38 ? OA5 CDL 506 C 1 HETATM 9 C CA3 CDL . . . BA 14 37.685 0.942 10.223 1 78.93 ? CA3 CDL 506 C 1 HETATM 10 C CA4 CDL . . . BA 14 36.364 0.231 10.228 1 92.44 ? CA4 CDL 506 C 1 HETATM 11 O OA6 CDL . . . BA 14 36.618 -1.025 9.619 1 108.82 ? OA6 CDL 506 C 1 HETATM 12 C CA5 CDL . . . BA 14 36.019 -2.136 10.313 1 108.31 ? CA5 CDL 506 C 1 HETATM 13 O OA7 CDL . . . BA 14 36.728 -3.1 10.539 1 105.96 ? OA7 CDL 506 C 1 HETATM 14 C C11 CDL . . . BA 14 34.56 -2.123 10.718 1 108.38 ? C11 CDL 506 C 1 HETATM 15 C C12 CDL . . . BA 14 33.998 -3.538 10.732 1 102.29 ? C12 CDL 506 C 1 HETATM 16 C CA6 CDL . . . BA 14 35.318 0.991 9.435 1 89.82 ? CA6 CDL 506 C 1 HETATM 17 O OA8 CDL . . . BA 14 35.521 0.7 8.054 1 88.55 ? OA8 CDL 506 C 1 HETATM 18 C CA7 CDL . . . BA 14 34.419 0.439 7.141 1 84.81 ? CA7 CDL 506 C 1 HETATM 19 O OA9 CDL . . . BA 14 33.311 0.905 7.361 1 74.05 ? OA9 CDL 506 C 1 HETATM 20 C C31 CDL . . . BA 14 34.651 -0.4 5.907 1 71.98 ? C31 CDL 506 C 1 HETATM 21 C CB2 CDL . . . BA 14 36.139 1.696 15.608 1 96.51 ? CB2 CDL 506 C 1 HETATM 22 O OB2 CDL . . . BA 14 35.051 1.264 16.382 1 95.22 ? OB2 CDL 506 C 1 HETATM 23 P PB2 CDL . . . BA 14 35.292 0.037 17.359 1 78.31 ? PB2 CDL 506 C 1 HETATM 24 O OB3 CDL . . . BA 14 34.171 0.042 18.357 1 70.46 ? OB3 CDL 506 C 1 HETATM 25 O OB4 CDL . . . BA 14 36.735 0.038 17.82 1 62.14 ? OB4 CDL 506 C 1 HETATM 26 O OB5 CDL . . . BA 14 35.069 -1.132 16.302 1 69.62 ? OB5 CDL 506 C 1 HETATM 27 C CB3 CDL . . . BA 14 35.79 -2.326 16.45 1 69.24 ? CB3 CDL 506 C 1 HETATM 28 C CB4 CDL . . . BA 14 35.419 -3.161 15.241 1 68.26 ? CB4 CDL 506 C 1 HETATM 29 O OB6 CDL . . . BA 14 35.135 -4.489 15.694 1 65.75 ? OB6 CDL 506 C 1 HETATM 30 C CB5 CDL . . . BA 14 33.916 -5.12 15.188 1 64.87 ? CB5 CDL 506 C 1 HETATM 31 O OB7 CDL . . . BA 14 32.837 -4.835 15.691 1 60.81 ? OB7 CDL 506 C 1 HETATM 32 C C51 CDL . . . BA 14 33.98 -6.141 14.074 1 59.92 ? C51 CDL 506 C 1 HETATM 33 C CB6 CDL . . . BA 14 36.565 -3.172 14.24 1 67.95 ? CB6 CDL 506 C 1 HETATM 34 O OB8 CDL . . . BA 14 37.451 -4.229 14.605 1 65.65 ? OB8 CDL 506 C 1 HETATM 35 C CB7 CDL . . . BA 14 38.422 -4.714 13.643 1 74.15 ? CB7 CDL 506 C 1 HETATM 36 O OB9 CDL . . . BA 14 39.364 -3.996 13.35 1 76.84 ? OB9 CDL 506 C 1 HETATM 37 C C71 CDL . . . BA 14 38.274 -6.081 13.014 1 70.5 ? C71 CDL 506 C 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 37 #