data_7YB8 # _model_server_result.job_id iT25NbCtVgYqdLiqSU2GhA _model_server_result.datetime_utc '2024-11-30 04:55:16' _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 7yb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1004}' # _entry.id 7YB8 # _exptl.entry_id 7YB8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 148.114 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2-hydroxypentanedioic acid' _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 7YB8 _cell.length_a 49.879 _cell.length_b 91.063 _cell.length_c 122.351 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YB8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 F _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 disulf ? disulf1 A SG CYS 312 A CYS 641 1_555 A SG CYS 319 A CYS 648 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 B SG CYS 16 B CYS 101 1_555 B SG CYS 25 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A NE2 HIS 350 A HIS 679 1_555 E MN MN . A MN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc2 A NE2 HIS 396 A HIS 725 1_555 E MN MN . A MN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc3 E MN MN . A MN 1003 1_555 F O3 2HG . A 2HG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc4 E MN MN . A MN 1003 1_555 F O2 2HG . A 2HG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? # _chem_comp.formula 'C5 H8 O5' _chem_comp.formula_weight 148.114 _chem_comp.id 2HG _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2-hydroxypentanedioic acid' _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 O1 2HG doub 1 n n C1 C2 2HG sing 2 n n C1 O2 2HG sing 3 n n C2 C3 2HG sing 4 n n C2 O3 2HG sing 5 n n C3 C4 2HG sing 6 n n C4 C5 2HG sing 7 n n O4 C5 2HG doub 8 n n C5 O5 2HG sing 9 n n C2 H2 2HG sing 10 n n O2 HO2 2HG sing 11 n n C3 H3 2HG sing 12 n n C3 H3A 2HG sing 13 n n O3 HO3 2HG sing 14 n n C4 H4 2HG sing 15 n n C4 H4A 2HG sing 16 n n O5 HO5 2HG sing 17 n n # _atom_sites.entry_id 7YB8 _atom_sites.fract_transf_matrix[1][1] 0.020049 _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] 0.010981 _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] 0.008173 _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 GOL A 1 1001 1001 GOL GOL . D 3 GOL A 1 1002 1101 GOL GOL . E 4 MN A 1 1003 801 MN MN . F 5 2HG A 1 1004 901 2HG LIG . G 6 HOH A 1 1101 63 HOH HOH . G 6 HOH A 2 1102 106 HOH HOH . G 6 HOH A 3 1103 58 HOH HOH . G 6 HOH A 4 1104 5 HOH HOH . G 6 HOH A 5 1105 114 HOH HOH . G 6 HOH A 6 1106 60 HOH HOH . G 6 HOH A 7 1107 67 HOH HOH . G 6 HOH A 8 1108 54 HOH HOH . G 6 HOH A 9 1109 53 HOH HOH . G 6 HOH A 10 1110 62 HOH HOH . G 6 HOH A 11 1111 3 HOH HOH . G 6 HOH A 12 1112 20 HOH HOH . G 6 HOH A 13 1113 10 HOH HOH . G 6 HOH A 14 1114 8 HOH HOH . G 6 HOH A 15 1115 80 HOH HOH . G 6 HOH A 16 1116 32 HOH HOH . G 6 HOH A 17 1117 26 HOH HOH . G 6 HOH A 18 1118 45 HOH HOH . G 6 HOH A 19 1119 31 HOH HOH . G 6 HOH A 20 1120 69 HOH HOH . G 6 HOH A 21 1121 4 HOH HOH . G 6 HOH A 22 1122 14 HOH HOH . G 6 HOH A 23 1123 74 HOH HOH . G 6 HOH A 24 1124 48 HOH HOH . G 6 HOH A 25 1125 40 HOH HOH . G 6 HOH A 26 1126 124 HOH HOH . G 6 HOH A 27 1127 13 HOH HOH . G 6 HOH A 28 1128 77 HOH HOH . G 6 HOH A 29 1129 111 HOH HOH . G 6 HOH A 30 1130 17 HOH HOH . G 6 HOH A 31 1131 34 HOH HOH . G 6 HOH A 32 1132 47 HOH HOH . G 6 HOH A 33 1133 2 HOH HOH . G 6 HOH A 34 1134 28 HOH HOH . G 6 HOH A 35 1135 57 HOH HOH . G 6 HOH A 36 1136 36 HOH HOH . G 6 HOH A 37 1137 113 HOH HOH . G 6 HOH A 38 1138 30 HOH HOH . G 6 HOH A 39 1139 16 HOH HOH . G 6 HOH A 40 1140 24 HOH HOH . G 6 HOH A 41 1141 65 HOH HOH . G 6 HOH A 42 1142 103 HOH HOH . G 6 HOH A 43 1143 18 HOH HOH . G 6 HOH A 44 1144 46 HOH HOH . G 6 HOH A 45 1145 52 HOH HOH . G 6 HOH A 46 1146 23 HOH HOH . G 6 HOH A 47 1147 64 HOH HOH . G 6 HOH A 48 1148 81 HOH HOH . G 6 HOH A 49 1149 29 HOH HOH . G 6 HOH A 50 1150 86 HOH HOH . G 6 HOH A 51 1151 42 HOH HOH . G 6 HOH A 52 1152 12 HOH HOH . G 6 HOH A 53 1153 120 HOH HOH . G 6 HOH A 54 1154 72 HOH HOH . G 6 HOH A 55 1155 79 HOH HOH . G 6 HOH A 56 1156 39 HOH HOH . G 6 HOH A 57 1157 105 HOH HOH . G 6 HOH A 58 1158 56 HOH HOH . G 6 HOH A 59 1159 6 HOH HOH . G 6 HOH A 60 1160 123 HOH HOH . G 6 HOH A 61 1161 71 HOH HOH . G 6 HOH A 62 1162 130 HOH HOH . G 6 HOH A 63 1163 41 HOH HOH . G 6 HOH A 64 1164 55 HOH HOH . G 6 HOH A 65 1165 75 HOH HOH . G 6 HOH A 66 1166 25 HOH HOH . G 6 HOH A 67 1167 99 HOH HOH . G 6 HOH A 68 1168 89 HOH HOH . G 6 HOH A 69 1169 118 HOH HOH . G 6 HOH A 70 1170 110 HOH HOH . G 6 HOH A 71 1171 19 HOH HOH . G 6 HOH A 72 1172 121 HOH HOH . G 6 HOH A 73 1173 15 HOH HOH . G 6 HOH A 74 1174 43 HOH HOH . G 6 HOH A 75 1175 78 HOH HOH . G 6 HOH A 76 1176 122 HOH HOH . G 6 HOH A 77 1177 90 HOH HOH . G 6 HOH A 78 1178 49 HOH HOH . G 6 HOH A 79 1179 68 HOH HOH . G 6 HOH A 80 1180 104 HOH HOH . G 6 HOH A 81 1181 107 HOH HOH . G 6 HOH A 82 1182 131 HOH HOH . G 6 HOH A 83 1183 11 HOH HOH . G 6 HOH A 84 1184 109 HOH HOH . G 6 HOH A 85 1185 92 HOH HOH . G 6 HOH A 86 1186 116 HOH HOH . G 6 HOH A 87 1187 91 HOH HOH . G 6 HOH A 88 1188 112 HOH HOH . G 6 HOH A 89 1189 93 HOH HOH . G 6 HOH A 90 1190 132 HOH HOH . G 6 HOH A 91 1191 87 HOH HOH . G 6 HOH A 92 1192 83 HOH HOH . G 6 HOH A 93 1193 134 HOH HOH . G 6 HOH A 94 1194 127 HOH HOH . G 6 HOH A 95 1195 128 HOH HOH . G 6 HOH A 96 1196 94 HOH HOH . G 6 HOH A 97 1197 33 HOH HOH . G 6 HOH A 98 1198 129 HOH HOH . G 6 HOH A 99 1199 82 HOH HOH . G 6 HOH A 100 1200 133 HOH HOH . G 6 HOH A 101 1201 98 HOH HOH . G 6 HOH A 102 1202 85 HOH HOH . G 6 HOH A 103 1203 44 HOH HOH . G 6 HOH A 104 1204 102 HOH HOH . G 6 HOH A 105 1205 76 HOH HOH . G 6 HOH A 106 1206 115 HOH HOH . G 6 HOH A 107 1207 108 HOH HOH . G 6 HOH A 108 1208 50 HOH HOH . G 6 HOH A 109 1209 66 HOH HOH . H 6 HOH B 1 201 96 HOH HOH . H 6 HOH B 2 202 1 HOH HOH . H 6 HOH B 3 203 61 HOH HOH . H 6 HOH B 4 204 38 HOH HOH . H 6 HOH B 5 205 100 HOH HOH . H 6 HOH B 6 206 27 HOH HOH . H 6 HOH B 7 207 119 HOH HOH . H 6 HOH B 8 208 125 HOH HOH . H 6 HOH B 9 209 101 HOH HOH . H 6 HOH B 10 210 126 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 2HG . . . F 5 56.797 17.545 16.567 1 111.04 ? C1 2HG 1004 A 1 HETATM 2 O O1 2HG . . . F 5 55.85 17.73 15.785 1 115.12 ? O1 2HG 1004 A 1 HETATM 3 C C2 2HG . . . F 5 57.999 16.765 16.054 1 98.58 ? C2 2HG 1004 A 1 HETATM 4 O O2 2HG . . . F 5 56.714 18 17.738 1 111.47 -1 O2 2HG 1004 A 1 HETATM 5 C C3 2HG . . . F 5 58.617 17.44 14.835 1 93.9 ? C3 2HG 1004 A 1 HETATM 6 O O3 2HG . . . F 5 58.961 16.751 17.055 1 87.51 ? O3 2HG 1004 A 1 HETATM 7 C C4 2HG . . . F 5 57.809 17.226 13.568 1 86.95 ? C4 2HG 1004 A 1 HETATM 8 O O4 2HG . . . F 5 58.801 17.268 11.381 1 75.65 -1 O4 2HG 1004 A 1 HETATM 9 C C5 2HG . . . F 5 58.455 17.912 12.388 1 78.29 ? C5 2HG 1004 A 1 HETATM 10 O O5 2HG . . . F 5 58.62 19.144 12.378 1 75.18 ? O5 2HG 1004 A 1 HETATM 11 H H2 2HG . . . F 5 57.674 15.769 15.781 1 118.92 ? H2 2HG 1004 A 1 HETATM 12 H H3 2HG . . . F 5 59.613 17.042 14.684 1 113.31 ? H3 2HG 1004 A 1 HETATM 13 H H3A 2HG . . . F 5 58.69 18.504 15.026 1 113.31 ? H3A 2HG 1004 A 1 HETATM 14 H HO3 2HG . . . F 5 59.134 17.63 17.352 1 105.64 ? HO3 2HG 1004 A 1 HETATM 15 H H4 2HG . . . F 5 57.737 16.165 13.367 1 104.96 ? H4 2HG 1004 A 1 HETATM 16 H H4A 2HG . . . F 5 56.812 17.625 13.71 1 104.96 ? H4A 2HG 1004 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 214 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 16 #