data_4XR1 # _model_server_result.job_id Qobi9hUVBSKuuvJiaL--Bg _model_server_result.datetime_utc '2024-10-18 15:28:07' _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 4xr1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1007}' # _entry.id 4XR1 # _exptl.entry_id 4XR1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _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 4XR1 _cell.length_a 64.811 _cell.length_b 64.811 _cell.length_c 246.706 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XR1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id J _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 hydrog WATSON-CRICK hydrog1 B N1 DA 3 B DA 312 1_555 C N3 DT 15 C DT 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 3 B DA 312 1_555 C O4 DT 15 C DT 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 4 B DG 313 1_555 C N3 DC 14 C DC 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 4 B DG 313 1_555 C O2 DC 14 C DC 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 4 B DG 313 1_555 C N4 DC 14 C DC 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 5 B DT 314 1_555 C N1 DA 13 C DA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 5 B DT 314 1_555 C N6 DA 13 C DA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DT 6 B DT 315 1_555 C N1 DA 12 C DA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O4 DT 6 B DT 315 1_555 C N6 DA 12 C DA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 7 B DA 316 1_555 C N3 DT 11 C DT 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 7 B DA 316 1_555 C O4 DT 11 C DT 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DC 8 B DC 317 1_555 C N1 DG 10 C DG 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N4 DC 8 B DC 317 1_555 C O6 DG 10 C DG 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O2 DC 8 B DC 317 1_555 C N2 DG 10 C DG 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DA 9 B DA 318 1_555 C N3 DT 9 C DT 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N6 DA 9 B DA 318 1_555 C O4 DT 9 C DT 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 DA 10 B DA 319 1_555 C N3 DT 8 C DT 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N6 DA 10 B DA 319 1_555 C O4 DT 8 C DT 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DC 11 B DC 320 1_555 C N1 DG 7 C DG 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N4 DC 11 B DC 320 1_555 C O6 DG 7 C DG 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O2 DC 11 B DC 320 1_555 C N2 DG 7 C DG 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DA 12 B DA 321 1_555 C N3 DT 6 C DT 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N6 DA 12 B DA 321 1_555 C O4 DT 6 C DT 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DT 13 B DT 322 1_555 C N1 DA 5 C DA 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O4 DT 13 B DT 322 1_555 C N6 DA 5 C DA 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 C2 MPD sing 386 n n C1 H11 MPD sing 387 n n C1 H12 MPD sing 388 n n C1 H13 MPD sing 389 n n C2 O2 MPD sing 390 n n C2 CM MPD sing 391 n n C2 C3 MPD sing 392 n n O2 HO2 MPD sing 393 n n CM HM1 MPD sing 394 n n CM HM2 MPD sing 395 n n CM HM3 MPD sing 396 n n C3 C4 MPD sing 397 n n C3 H31 MPD sing 398 n n C3 H32 MPD sing 399 n n C4 O4 MPD sing 400 n n C4 C5 MPD sing 401 n n C4 H4 MPD sing 402 n n O4 HO4 MPD sing 403 n n C5 H51 MPD sing 404 n n C5 H52 MPD sing 405 n n C5 H53 MPD sing 406 n n # _atom_sites.entry_id 4XR1 _atom_sites.fract_transf_matrix[1][1] 0.015429 _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] 0.015429 _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] 0.004053 _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 D 4 IOD A 1 1001 1001 IOD IOD . E 4 IOD A 1 1002 1002 IOD IOD . F 4 IOD A 1 1003 1003 IOD IOD . G 4 IOD A 1 1004 1004 IOD IOD . H 4 IOD A 1 1005 1005 IOD IOD . I 4 IOD A 1 1006 1006 IOD IOD . J 5 MPD A 1 1007 1007 MPD MPD . K 6 HOH A 1 1101 63 HOH HOH . K 6 HOH A 2 1102 45 HOH HOH . K 6 HOH A 3 1103 18 HOH HOH . K 6 HOH A 4 1104 37 HOH HOH . K 6 HOH A 5 1105 76 HOH HOH . K 6 HOH A 6 1106 101 HOH HOH . K 6 HOH A 7 1107 107 HOH HOH . K 6 HOH A 8 1108 72 HOH HOH . K 6 HOH A 9 1109 64 HOH HOH . K 6 HOH A 10 1110 75 HOH HOH . K 6 HOH A 11 1111 87 HOH HOH . K 6 HOH A 12 1112 83 HOH HOH . K 6 HOH A 13 1113 100 HOH HOH . K 6 HOH A 14 1114 86 HOH HOH . K 6 HOH A 15 1115 66 HOH HOH . K 6 HOH A 16 1116 102 HOH HOH . K 6 HOH A 17 1117 109 HOH HOH . K 6 HOH A 18 1118 94 HOH HOH . K 6 HOH A 19 1119 8 HOH HOH . K 6 HOH A 20 1120 14 HOH HOH . K 6 HOH A 21 1121 15 HOH HOH . K 6 HOH A 22 1122 17 HOH HOH . K 6 HOH A 23 1123 19 HOH HOH . K 6 HOH A 24 1124 20 HOH HOH . K 6 HOH A 25 1125 23 HOH HOH . K 6 HOH A 26 1126 24 HOH HOH . K 6 HOH A 27 1127 26 HOH HOH . K 6 HOH A 28 1128 27 HOH HOH . K 6 HOH A 29 1129 28 HOH HOH . K 6 HOH A 30 1130 30 HOH HOH . K 6 HOH A 31 1131 31 HOH HOH . K 6 HOH A 32 1132 32 HOH HOH . K 6 HOH A 33 1133 33 HOH HOH . K 6 HOH A 34 1134 34 HOH HOH . K 6 HOH A 35 1135 35 HOH HOH . K 6 HOH A 36 1136 36 HOH HOH . K 6 HOH A 37 1137 38 HOH HOH . K 6 HOH A 38 1138 39 HOH HOH . K 6 HOH A 39 1139 41 HOH HOH . K 6 HOH A 40 1140 42 HOH HOH . K 6 HOH A 41 1141 43 HOH HOH . K 6 HOH A 42 1142 44 HOH HOH . K 6 HOH A 43 1143 46 HOH HOH . K 6 HOH A 44 1144 47 HOH HOH . K 6 HOH A 45 1145 51 HOH HOH . K 6 HOH A 46 1146 52 HOH HOH . K 6 HOH A 47 1147 54 HOH HOH . K 6 HOH A 48 1148 55 HOH HOH . K 6 HOH A 49 1149 57 HOH HOH . K 6 HOH A 50 1150 58 HOH HOH . K 6 HOH A 51 1151 59 HOH HOH . K 6 HOH A 52 1152 68 HOH HOH . K 6 HOH A 53 1153 70 HOH HOH . K 6 HOH A 54 1154 73 HOH HOH . K 6 HOH A 55 1155 77 HOH HOH . K 6 HOH A 56 1156 78 HOH HOH . K 6 HOH A 57 1157 80 HOH HOH . K 6 HOH A 58 1158 85 HOH HOH . K 6 HOH A 59 1159 88 HOH HOH . K 6 HOH A 60 1160 90 HOH HOH . K 6 HOH A 61 1161 91 HOH HOH . K 6 HOH A 62 1162 92 HOH HOH . K 6 HOH A 63 1163 93 HOH HOH . K 6 HOH A 64 1164 95 HOH HOH . K 6 HOH A 65 1165 96 HOH HOH . K 6 HOH A 66 1166 97 HOH HOH . K 6 HOH A 67 1167 98 HOH HOH . K 6 HOH A 68 1168 103 HOH HOH . K 6 HOH A 69 1169 105 HOH HOH . K 6 HOH A 70 1170 110 HOH HOH . K 6 HOH A 71 1171 111 HOH HOH . K 6 HOH A 72 1172 112 HOH HOH . L 6 HOH B 1 401 69 HOH HOH . L 6 HOH B 2 402 22 HOH HOH . L 6 HOH B 3 403 29 HOH HOH . L 6 HOH B 4 404 53 HOH HOH . L 6 HOH B 5 405 56 HOH HOH . L 6 HOH B 6 406 67 HOH HOH . L 6 HOH B 7 407 74 HOH HOH . L 6 HOH B 8 408 79 HOH HOH . L 6 HOH B 9 409 81 HOH HOH . L 6 HOH B 10 410 82 HOH HOH . L 6 HOH B 11 411 89 HOH HOH . L 6 HOH B 12 412 106 HOH HOH . L 6 HOH B 13 413 108 HOH HOH . M 6 HOH C 1 401 1 HOH HOH . M 6 HOH C 2 402 11 HOH HOH . M 6 HOH C 3 403 25 HOH HOH . M 6 HOH C 4 404 40 HOH HOH . M 6 HOH C 5 405 48 HOH HOH . M 6 HOH C 6 406 50 HOH HOH . M 6 HOH C 7 407 62 HOH HOH . M 6 HOH C 8 408 71 HOH HOH . M 6 HOH C 9 409 84 HOH HOH . M 6 HOH C 10 410 99 HOH HOH . M 6 HOH C 11 411 104 HOH HOH . # 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 MPD . . . J 5 -2.581 -33.177 -13.802 1 49.67 ? C1 MPD 1007 A 1 HETATM 2 C C2 MPD . . . J 5 -1.241 -32.359 -14.11 1 71.32 ? C2 MPD 1007 A 1 HETATM 3 O O2 MPD . . . J 5 -0.639 -31.722 -13.013 1 79.56 ? O2 MPD 1007 A 1 HETATM 4 C CM MPD . . . J 5 0.086 -33.188 -14.331 1 59.84 ? CM MPD 1007 A 1 HETATM 5 C C3 MPD . . . J 5 -1.564 -31.026 -14.872 1 57.28 ? C3 MPD 1007 A 1 HETATM 6 C C4 MPD . . . J 5 -1.869 -31.06 -16.367 1 67.08 ? C4 MPD 1007 A 1 HETATM 7 O O4 MPD . . . J 5 -0.596 -31.389 -17.045 1 59.09 ? O4 MPD 1007 A 1 HETATM 8 C C5 MPD . . . J 5 -3.058 -32.033 -16.601 1 46.73 ? C5 MPD 1007 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 8 #