data_5NMI # _model_server_result.job_id 4dvXAhM3K_MneQVsEzOfIQ _model_server_result.datetime_utc '2024-11-23 12:20:13' _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":"EA","auth_seq_id":503}' # _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 . . . EA 14 45.251 0.693 15.239 1 109.72 ? C1 CDL 503 D 1 HETATM 2 O O1 CDL . . . EA 14 44.584 1.954 15.362 1 100.06 ? O1 CDL 503 D 1 HETATM 3 C CA2 CDL . . . EA 14 44.303 -0.429 15.651 1 109.47 ? CA2 CDL 503 D 1 HETATM 4 O OA2 CDL . . . EA 14 44.962 -1.682 15.472 1 116.58 ? OA2 CDL 503 D 1 HETATM 5 P PA1 CDL . . . EA 14 44.712 -2.984 16.387 1 102.68 ? PA1 CDL 503 D 1 HETATM 6 O OA3 CDL . . . EA 14 43.508 -2.755 17.27 1 91.79 ? OA3 CDL 503 D 1 HETATM 7 O OA4 CDL . . . EA 14 44.743 -4.176 15.461 1 89.11 ? OA4 CDL 503 D 1 HETATM 8 O OA5 CDL . . . EA 14 46.015 -3.046 17.334 1 86.52 ? OA5 CDL 503 D 1 HETATM 9 C CA3 CDL . . . EA 14 47.32 -2.72 16.86 1 82.7 ? CA3 CDL 503 D 1 HETATM 10 C CA4 CDL . . . EA 14 48.323 -2.932 17.989 1 89.06 ? CA4 CDL 503 D 1 HETATM 11 O OA6 CDL . . . EA 14 47.871 -2.269 19.172 1 82.63 ? OA6 CDL 503 D 1 HETATM 12 C C11 CDL . . . EA 14 44.358 -14.935 1.136 1 42.31 ? C11 CDL 503 D 1 HETATM 13 C C12 CDL . . . EA 14 43.429 -14.141 0.221 1 46.68 ? C12 CDL 503 D 1 HETATM 14 C C13 CDL . . . EA 14 43.051 -14.942 -1.01 1 45.44 ? C13 CDL 503 D 1 HETATM 15 C CA6 CDL . . . EA 14 49.689 -2.398 17.58 1 95.02 ? CA6 CDL 503 D 1 HETATM 16 O OA8 CDL . . . EA 14 50.499 -2.209 18.74 1 115.51 ? OA8 CDL 503 D 1 HETATM 17 C CB2 CDL . . . EA 14 45.725 0.489 13.804 1 112.29 ? CB2 CDL 503 D 1 HETATM 18 O OB2 CDL . . . EA 14 44.771 0.993 12.88 1 108.7 ? OB2 CDL 503 D 1 HETATM 19 P PB2 CDL . . . EA 14 44.993 0.715 11.309 1 95.34 ? PB2 CDL 503 D 1 HETATM 20 O OB3 CDL . . . EA 14 46.312 1.331 10.9 1 89.59 ? OB3 CDL 503 D 1 HETATM 21 O OB4 CDL . . . EA 14 44.736 -0.749 11.048 1 97.47 ? OB4 CDL 503 D 1 HETATM 22 O OB5 CDL . . . EA 14 43.789 1.551 10.649 1 84.96 ? OB5 CDL 503 D 1 HETATM 23 C CB3 CDL . . . EA 14 43.874 2.067 9.324 1 80.02 ? CB3 CDL 503 D 1 HETATM 24 C CB4 CDL . . . EA 14 42.713 1.541 8.494 1 85.4 ? CB4 CDL 503 D 1 HETATM 25 O OB6 CDL . . . EA 14 42.805 0.116 8.412 1 87.45 ? OB6 CDL 503 D 1 HETATM 26 C CB5 CDL . . . EA 14 41.657 -0.509 7.77 1 88.03 ? CB5 CDL 503 D 1 HETATM 27 O OB7 CDL . . . EA 14 40.558 -0.425 8.29 1 77.85 ? OB7 CDL 503 D 1 HETATM 28 C C51 CDL . . . EA 14 41.831 -1.244 6.465 1 83.63 ? C51 CDL 503 D 1 HETATM 29 C C52 CDL . . . EA 14 43.11 -2.074 6.487 1 77.23 ? C52 CDL 503 D 1 HETATM 30 C C53 CDL . . . EA 14 43.239 -2.932 5.236 1 70.79 ? C53 CDL 503 D 1 HETATM 31 C C54 CDL . . . EA 14 44.476 -3.821 5.308 1 72.2 ? C54 CDL 503 D 1 HETATM 32 C C55 CDL . . . EA 14 44.964 -4.217 3.919 1 68.46 ? C55 CDL 503 D 1 HETATM 33 C CB6 CDL . . . EA 14 42.762 2.193 7.112 1 87.25 ? CB6 CDL 503 D 1 HETATM 34 O OB8 CDL . . . EA 14 41.564 2.932 6.898 1 95.09 ? OB8 CDL 503 D 1 HETATM 35 C CB7 CDL . . . EA 14 40.956 2.964 5.583 1 107.08 ? CB7 CDL 503 D 1 HETATM 36 O OB9 CDL . . . EA 14 41.466 3.656 4.715 1 113.48 ? OB9 CDL 503 D 1 HETATM 37 C C71 CDL . . . EA 14 39.719 2.136 5.324 1 98.83 ? C71 CDL 503 D 1 HETATM 38 C C72 CDL . . . EA 14 38.732 2.895 4.445 1 84.45 ? C72 CDL 503 D 1 HETATM 39 C C73 CDL . . . EA 14 37.443 2.096 4.27 1 80.29 ? C73 CDL 503 D 1 HETATM 40 C C74 CDL . . . EA 14 36.738 2.389 2.946 1 73.89 ? C74 CDL 503 D 1 HETATM 41 C C75 CDL . . . EA 14 36.382 1.102 2.215 1 68.14 ? C75 CDL 503 D 1 HETATM 42 C C76 CDL . . . EA 14 35.514 1.397 1 1 64.65 ? C76 CDL 503 D 1 HETATM 43 C C77 CDL . . . EA 14 35.079 0.114 0.293 1 61.93 ? C77 CDL 503 D 1 HETATM 44 C C78 CDL . . . EA 14 33.61 0.171 -0.114 1 57.34 ? C78 CDL 503 D 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 44 #