data_3WMQ # _model_server_result.job_id nfaZnzIrjG3dN4ecoYrPfA _model_server_result.datetime_utc '2024-11-26 00:41:35' _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 3wmq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1005}' # _entry.id 3WMQ # _exptl.entry_id 3WMQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 2 _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 3WMQ _cell.length_a 154.246 _cell.length_b 154.246 _cell.length_c 154.246 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WMQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 211 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 4 'crystal symmetry operation' 38_444 -y-1/2,-x-1/2,-z-1/2 0 -1 0 -1 0 0 0 0 -1 -77.123 -77.123 -77.123 5 'crystal symmetry operation' 43_444 -x-1/2,-z-1/2,-y-1/2 -1 0 0 0 0 -1 0 -1 0 -77.123 -77.123 -77.123 6 'crystal symmetry operation' 48_444 -z-1/2,-y-1/2,-x-1/2 0 0 -1 0 -1 0 -1 0 0 -77.123 -77.123 -77.123 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 1001 NAG 2 n B NAG 2 B 2 NAG A 1002 NAG # 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 A SG CYS 8 A CYS 8 1_555 A SG CYS 93 A CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 17 A CYS 17 1_555 A SG CYS 22 A CYS 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 60 A ASN 60 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? metalc ? metalc1 J NA NA . A NA 1010 1_555 K O HOH . A HOH 1148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.071 ? metalc ? metalc2 J NA NA . A NA 1010 1_555 K O HOH . A HOH 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? # _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 248 n n C1 H11 MPD sing 249 n n C1 H12 MPD sing 250 n n C1 H13 MPD sing 251 n n C2 O2 MPD sing 252 n n C2 CM MPD sing 253 n n C2 C3 MPD sing 254 n n O2 HO2 MPD sing 255 n n CM HM1 MPD sing 256 n n CM HM2 MPD sing 257 n n CM HM3 MPD sing 258 n n C3 C4 MPD sing 259 n n C3 H31 MPD sing 260 n n C3 H32 MPD sing 261 n n C4 O4 MPD sing 262 n n C4 C5 MPD sing 263 n n C4 H4 MPD sing 264 n n O4 HO4 MPD sing 265 n n C5 H51 MPD sing 266 n n C5 H52 MPD sing 267 n n C5 H53 MPD sing 268 n n # _atom_sites.entry_id 3WMQ _atom_sites.fract_transf_matrix[1][1] 0.006483 _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] 0.006483 _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] 0.006483 _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 C 3 A2G A 1 1003 1003 A2G A2G . D 4 MPD A 1 1004 1004 MPD MPD . E 4 MPD A 1 1005 1005 MPD MPD . F 5 CL A 1 1006 1006 CL CL . G 5 CL A 1 1007 1007 CL CL . H 5 CL A 1 1008 1008 CL CL . I 5 CL A 1 1009 1009 CL CL . J 6 NA A 1 1010 1010 NA NA . K 7 HOH A 1 1101 1101 HOH HOH . K 7 HOH A 2 1102 1102 HOH HOH . K 7 HOH A 3 1103 1103 HOH HOH . K 7 HOH A 4 1104 1104 HOH HOH . K 7 HOH A 5 1105 1105 HOH HOH . K 7 HOH A 6 1106 1106 HOH HOH . K 7 HOH A 7 1107 1107 HOH HOH . K 7 HOH A 8 1108 1108 HOH HOH . K 7 HOH A 9 1109 1109 HOH HOH . K 7 HOH A 10 1110 1110 HOH HOH . K 7 HOH A 11 1111 1111 HOH HOH . K 7 HOH A 12 1112 1112 HOH HOH . K 7 HOH A 13 1113 1113 HOH HOH . K 7 HOH A 14 1114 1114 HOH HOH . K 7 HOH A 15 1115 1115 HOH HOH . K 7 HOH A 16 1116 1116 HOH HOH . K 7 HOH A 17 1117 1117 HOH HOH . K 7 HOH A 18 1118 1118 HOH HOH . K 7 HOH A 19 1119 1119 HOH HOH . K 7 HOH A 20 1120 1121 HOH HOH . K 7 HOH A 21 1121 1122 HOH HOH . K 7 HOH A 22 1122 1123 HOH HOH . K 7 HOH A 23 1123 1124 HOH HOH . K 7 HOH A 24 1124 1125 HOH HOH . K 7 HOH A 25 1125 1126 HOH HOH . K 7 HOH A 26 1126 1127 HOH HOH . K 7 HOH A 27 1127 1128 HOH HOH . K 7 HOH A 28 1128 1129 HOH HOH . K 7 HOH A 29 1129 1130 HOH HOH . K 7 HOH A 30 1130 1131 HOH HOH . K 7 HOH A 31 1131 1132 HOH HOH . K 7 HOH A 32 1132 1133 HOH HOH . K 7 HOH A 33 1133 1134 HOH HOH . K 7 HOH A 34 1134 1135 HOH HOH . K 7 HOH A 35 1135 1136 HOH HOH . K 7 HOH A 36 1136 1137 HOH HOH . K 7 HOH A 37 1137 1138 HOH HOH . K 7 HOH A 38 1138 1139 HOH HOH . K 7 HOH A 39 1139 1140 HOH HOH . K 7 HOH A 40 1140 1141 HOH HOH . K 7 HOH A 41 1141 1142 HOH HOH . K 7 HOH A 42 1142 1143 HOH HOH . K 7 HOH A 43 1143 1144 HOH HOH . K 7 HOH A 44 1144 1145 HOH HOH . K 7 HOH A 45 1145 1146 HOH HOH . K 7 HOH A 46 1146 1147 HOH HOH . K 7 HOH A 47 1147 1148 HOH HOH . K 7 HOH A 48 1148 1150 HOH HOH . K 7 HOH A 49 1149 1151 HOH HOH . K 7 HOH A 50 1150 1152 HOH HOH . K 7 HOH A 51 1151 1153 HOH HOH . K 7 HOH A 52 1152 1154 HOH HOH . K 7 HOH A 53 1153 1155 HOH HOH . K 7 HOH A 54 1154 1156 HOH HOH . K 7 HOH A 55 1155 1157 HOH HOH . K 7 HOH A 56 1156 1159 HOH HOH . K 7 HOH A 57 1157 1160 HOH HOH . K 7 HOH A 58 1158 1161 HOH HOH . K 7 HOH A 59 1159 1162 HOH HOH . K 7 HOH A 60 1160 1163 HOH HOH . K 7 HOH A 61 1161 1164 HOH HOH . K 7 HOH A 62 1162 1165 HOH HOH . K 7 HOH A 63 1163 1166 HOH HOH . K 7 HOH A 64 1164 1167 HOH HOH . K 7 HOH A 65 1165 1168 HOH HOH . K 7 HOH A 66 1166 1169 HOH HOH . K 7 HOH A 67 1167 1170 HOH HOH . K 7 HOH A 68 1168 1171 HOH HOH . K 7 HOH A 69 1169 1172 HOH HOH . K 7 HOH A 70 1170 1173 HOH HOH . K 7 HOH A 71 1171 1174 HOH HOH . K 7 HOH A 72 1172 1175 HOH HOH . K 7 HOH A 73 1173 1176 HOH HOH . K 7 HOH A 74 1174 1177 HOH HOH . K 7 HOH A 75 1175 1178 HOH HOH . K 7 HOH A 76 1176 1179 HOH HOH . K 7 HOH A 77 1177 1180 HOH HOH . K 7 HOH A 78 1178 1181 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 . . . E 4 -28.193 -5.642 -0.686 1 55.63 ? C1 MPD 1005 A 1 HETATM 2 C C2 MPD . . . E 4 -27.643 -4.265 -0.431 1 56.12 ? C2 MPD 1005 A 1 HETATM 3 O O2 MPD . . . E 4 -26.676 -3.981 -1.458 1 55.73 ? O2 MPD 1005 A 1 HETATM 4 C CM MPD . . . E 4 -28.746 -3.274 -0.467 1 55.7 ? CM MPD 1005 A 1 HETATM 5 C C3 MPD . . . E 4 -26.996 -4.229 0.973 1 56.02 ? C3 MPD 1005 A 1 HETATM 6 C C4 MPD . . . E 4 -25.507 -3.921 1.171 1 56.38 ? C4 MPD 1005 A 1 HETATM 7 O O4 MPD . . . E 4 -25.203 -2.619 0.709 1 56.82 ? O4 MPD 1005 A 1 HETATM 8 C C5 MPD . . . E 4 -25.131 -4.004 2.647 1 56.16 ? C5 MPD 1005 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 8 #