data_5M7J # _model_server_result.job_id NVIheG1ULScU4hjM5oqD6A _model_server_result.datetime_utc '2024-11-08 13:31:49' _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 5m7j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":405}' # _entry.id 5M7J # _exptl.entry_id 5M7J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 722.911 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE' _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 5M7J _cell.length_a 57.9 _cell.length_b 84.8 _cell.length_c 384.3 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M7J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_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 _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 # _struct_asym.details ? _struct_asym.entity_id 13 _struct_asym.id U _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 D C FME 1 D FME 1 1_555 D N TYR 2 D TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A NE2 HIS 111 A HIS 91 1_555 E FE HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc2 A NE2 HIS 144 A HIS 124 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc3 A NE2 HIS 156 A HIS 136 1_555 F FE HEC . A HEC 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc4 A NE2 HIS 268 A HIS 248 1_555 G FE HEC . A HEC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc5 A NE2 HIS 329 A HIS 309 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc6 B NE2 HIS 191 B HIS 190 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc7 B NE2 HIS 231 B HIS 230 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc8 P FE FE2 . B FE2 307 1_555 C NE2 HIS 218 C HIS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc9 P FE FE2 . B FE2 307 1_555 C OE1 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc10 P FE FE2 . B FE2 307 1_555 C OE2 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc11 P FE FE2 . B FE2 307 1_555 C NE2 HIS 265 C HIS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? # _chem_comp.formula 'C40 H68 O7 P2' _chem_comp.formula_weight 722.911 _chem_comp.id OTP _chem_comp.mon_nstd_flag . _chem_comp.name '(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'OCTAPRENYL PYROPHOSPHATE' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O7 P2 OTP sing 1027 n n O7 HO7 OTP sing 1028 n n P2 O5 OTP doub 1029 n n P2 O6 OTP sing 1030 n n P2 O4 OTP sing 1031 n n O6 HO6 OTP sing 1032 n n O4 P1 OTP sing 1033 n n P1 O2 OTP doub 1034 n n P1 O3 OTP sing 1035 n n P1 O1 OTP sing 1036 n n O3 HO3 OTP sing 1037 n n O1 C40 OTP sing 1038 n n C40 C39 OTP sing 1039 n n C40 H401 OTP sing 1040 n n C40 H402 OTP sing 1041 n n C39 C37 OTP doub 1042 e n C39 H39 OTP sing 1043 n n C37 C38 OTP sing 1044 n n C37 C36 OTP sing 1045 n n C38 H381 OTP sing 1046 n n C38 H382 OTP sing 1047 n n C38 H383 OTP sing 1048 n n C36 C35 OTP sing 1049 n n C36 H361 OTP sing 1050 n n C36 H362 OTP sing 1051 n n C35 C34 OTP sing 1052 n n C35 H351 OTP sing 1053 n n C35 H352 OTP sing 1054 n n C34 C32 OTP doub 1055 e n C34 H34 OTP sing 1056 n n C32 C33 OTP sing 1057 n n C32 C31 OTP sing 1058 n n C33 H331 OTP sing 1059 n n C33 H332 OTP sing 1060 n n C33 H333 OTP sing 1061 n n C31 C30 OTP sing 1062 n n C31 H311 OTP sing 1063 n n C31 H312 OTP sing 1064 n n C30 C29 OTP sing 1065 n n C30 H301 OTP sing 1066 n n C30 H302 OTP sing 1067 n n C29 C27 OTP doub 1068 e n C29 H29 OTP sing 1069 n n C27 C28 OTP sing 1070 n n C27 C26 OTP sing 1071 n n C28 H281 OTP sing 1072 n n C28 H282 OTP sing 1073 n n C28 H283 OTP sing 1074 n n C26 C25 OTP sing 1075 n n C26 H261 OTP sing 1076 n n C26 H262 OTP sing 1077 n n C25 C24 OTP sing 1078 n n C25 H251 OTP sing 1079 n n C25 H252 OTP sing 1080 n n C24 C22 OTP doub 1081 e n C24 H24 OTP sing 1082 n n C22 C23 OTP sing 1083 n n C22 C21 OTP sing 1084 n n C23 H231 OTP sing 1085 n n C23 H232 OTP sing 1086 n n C23 H233 OTP sing 1087 n n C21 C20 OTP sing 1088 n n C21 H211 OTP sing 1089 n n C21 H212 OTP sing 1090 n n C20 C19 OTP sing 1091 n n C20 H201 OTP sing 1092 n n C20 H202 OTP sing 1093 n n C19 C17 OTP doub 1094 e n C19 H19 OTP sing 1095 n n C17 C18 OTP sing 1096 n n C17 C16 OTP sing 1097 n n C18 H181 OTP sing 1098 n n C18 H182 OTP sing 1099 n n C18 H183 OTP sing 1100 n n C16 C15 OTP sing 1101 n n C16 H161 OTP sing 1102 n n C16 H162 OTP sing 1103 n n C15 C14 OTP sing 1104 n n C15 H151 OTP sing 1105 n n C15 H152 OTP sing 1106 n n C14 C12 OTP doub 1107 e n C14 H14 OTP sing 1108 n n C12 C13 OTP sing 1109 n n C12 C11 OTP sing 1110 n n C13 H131 OTP sing 1111 n n C13 H132 OTP sing 1112 n n C13 H133 OTP sing 1113 n n C11 C10 OTP sing 1114 n n C11 H111 OTP sing 1115 n n C11 H112 OTP sing 1116 n n C10 C9 OTP sing 1117 n n C10 H101 OTP sing 1118 n n C10 H102 OTP sing 1119 n n C9 C7 OTP doub 1120 e n C9 H9 OTP sing 1121 n n C7 C8 OTP sing 1122 n n C7 C6 OTP sing 1123 n n C8 H81 OTP sing 1124 n n C8 H82 OTP sing 1125 n n C8 H83 OTP sing 1126 n n C6 C5 OTP sing 1127 n n C6 H61 OTP sing 1128 n n C6 H62 OTP sing 1129 n n C5 C4 OTP sing 1130 n n C5 H51 OTP sing 1131 n n C5 H52 OTP sing 1132 n n C4 C2 OTP doub 1133 n n C4 H4 OTP sing 1134 n n C2 C3 OTP sing 1135 n n C2 C1 OTP sing 1136 n n C3 H31 OTP sing 1137 n n C3 H32 OTP sing 1138 n n C3 H33 OTP sing 1139 n n C1 H11 OTP sing 1140 n n C1 H12 OTP sing 1141 n n C1 H13 OTP sing 1142 n n # _atom_sites.entry_id 5M7J _atom_sites.fract_transf_matrix[1][1] 0.017271 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011792 _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] 0.002602 _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 E 5 HEC A 1 401 1333 HEC HEM . F 5 HEC A 1 402 1334 HEC HEM . G 5 HEC A 1 403 1335 HEC HEM . H 5 HEC A 1 404 1336 HEC HEM . I 6 DGA A 1 405 1278 DGA DGA . J 7 BCL B 1 301 1274 BCL BCL . K 7 BCL B 1 302 1275 BCL BCL . L 7 BCL B 1 303 1276 BCL BCL . M 8 BPB B 1 304 1277 BPB BPB . N 9 MPG B 1 305 1279 MPG MPG . O 9 MPG B 1 306 1280 MPG MPG . P 10 FE2 B 1 307 1326 FE2 FE2 . Q 7 BCL C 1 401 1324 BCL BCL . R 8 BPB C 1 402 1325 BPB BPB . S 11 MQ7 C 1 403 1327 MQ7 MQ7 . T 12 NS5 C 1 404 1328 NS5 NS5 . U 13 OTP C 1 405 1329 OTP OTP . V 9 MPG C 1 406 1330 MPG MPG . W 14 PO4 C 1 407 1331 PO4 PO4 . X 14 PO4 C 1 408 1332 PO4 PO4 . # 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 O O1 OTP . . . U 13 16.71 -0.502 59.875 1 58.66 ? O1 OTP 405 C 1 HETATM 2 C C40 OTP . . . U 13 16.04 -1.658 59.43 1 60.17 ? C40 OTP 405 C 1 HETATM 3 C C39 OTP . . . U 13 17.046 -2.679 58.941 1 53.22 ? C39 OTP 405 C 1 HETATM 4 C C37 OTP . . . U 13 16.844 -4.003 59.112 1 52 ? C37 OTP 405 C 1 HETATM 5 C C38 OTP . . . U 13 17.88 -4.982 58.606 1 46.04 ? C38 OTP 405 C 1 HETATM 6 C C36 OTP . . . U 13 15.601 -4.523 59.81 1 52.09 ? C36 OTP 405 C 1 HETATM 7 C C35 OTP . . . U 13 14.462 -4.692 58.821 1 60.16 ? C35 OTP 405 C 1 HETATM 8 C C34 OTP . . . U 13 13.509 -5.773 59.285 1 60.82 ? C34 OTP 405 C 1 HETATM 9 C C32 OTP . . . U 13 12.233 -5.785 58.849 1 59.53 ? C32 OTP 405 C 1 HETATM 10 C C33 OTP . . . U 13 11.778 -4.688 57.907 1 60.98 ? C33 OTP 405 C 1 HETATM 11 C C31 OTP . . . U 13 11.311 -6.891 59.342 1 46.85 ? C31 OTP 405 C 1 HETATM 12 C C30 OTP . . . U 13 10.137 -7.219 58.439 1 41.14 ? C30 OTP 405 C 1 HETATM 13 C C29 OTP . . . U 13 10.571 -7.603 57.039 1 39.31 ? C29 OTP 405 C 1 HETATM 14 C C27 OTP . . . U 13 9.73 -8.256 56.216 1 40.89 ? C27 OTP 405 C 1 HETATM 15 C C28 OTP . . . U 13 8.349 -8.643 56.695 1 37.09 ? C28 OTP 405 C 1 HETATM 16 C C26 OTP . . . U 13 10.182 -8.613 54.818 1 44.31 ? C26 OTP 405 C 1 HETATM 17 C C25 OTP . . . U 13 9.757 -7.546 53.83 1 44.09 ? C25 OTP 405 C 1 HETATM 18 C C24 OTP . . . U 13 9.358 -8.245 52.549 1 45.32 ? C24 OTP 405 C 1 HETATM 19 C C22 OTP . . . U 13 8.738 -7.619 51.525 1 51.3 ? C22 OTP 405 C 1 HETATM 20 C C23 OTP . . . U 13 8.389 -6.147 51.594 1 52.71 ? C23 OTP 405 C 1 HETATM 21 C C21 OTP . . . U 13 8.383 -8.446 50.308 1 45.68 ? C21 OTP 405 C 1 HETATM 22 C C20 OTP . . . U 13 8.419 -7.677 49.006 1 46.05 ? C20 OTP 405 C 1 HETATM 23 C C19 OTP . . . U 13 8.393 -8.742 47.932 1 45.48 ? C19 OTP 405 C 1 HETATM 24 C C17 OTP . . . U 13 8.444 -8.494 46.608 1 62.7 ? C17 OTP 405 C 1 HETATM 25 C C18 OTP . . . U 13 8.407 -9.678 45.667 1 59.64 ? C18 OTP 405 C 1 HETATM 26 C C16 OTP . . . U 13 8.535 -7.083 46.06 1 73.41 ? C16 OTP 405 C 1 HETATM 27 C C15 OTP . . . U 13 9.42 -7.049 44.828 1 76.86 ? C15 OTP 405 C 1 HETATM 28 C C14 OTP . . . U 13 8.587 -7.024 43.559 1 73.91 ? C14 OTP 405 C 1 HETATM 29 C C12 OTP . . . U 13 8.895 -6.177 42.555 1 62.36 ? C12 OTP 405 C 1 HETATM 30 C C13 OTP . . . U 13 10.08 -5.248 42.705 1 75.05 ? C13 OTP 405 C 1 HETATM 31 C C11 OTP . . . U 13 8.061 -6.164 41.289 1 62.7 ? C11 OTP 405 C 1 HETATM 32 C C10 OTP . . . U 13 7.504 -4.781 41.021 1 72.67 ? C10 OTP 405 C 1 HETATM 33 C C9 OTP . . . U 13 8.351 -4.08 39.979 1 73.52 ? C9 OTP 405 C 1 HETATM 34 C C7 OTP . . . U 13 8.13 -2.788 39.659 1 79.32 ? C7 OTP 405 C 1 HETATM 35 C C8 OTP . . . U 13 7.022 -2.009 40.336 1 63.42 ? C8 OTP 405 C 1 HETATM 36 C C6 OTP . . . U 13 9.009 -2.13 38.615 1 90.45 ? C6 OTP 405 C 1 HETATM 37 C C5 OTP . . . U 13 8.411 -0.826 38.133 1 90.48 ? C5 OTP 405 C 1 HETATM 38 C C4 OTP . . . U 13 9.493 -0.023 37.443 1 85.48 ? C4 OTP 405 C 1 HETATM 39 C C2 OTP . . . U 13 9.182 1.006 36.628 1 74.21 ? C2 OTP 405 C 1 HETATM 40 C C3 OTP . . . U 13 10.285 1.79 35.952 1 69.3 ? C3 OTP 405 C 1 HETATM 41 C C1 OTP . . . U 13 7.735 1.377 36.389 1 71.71 ? C1 OTP 405 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 35 _model_server_stats.element_count 41 #