data_8VDD # _model_server_result.job_id NxC6R3u6osqiat-mqLFo4Q _model_server_result.datetime_utc '2024-11-16 18:43:09' _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 8vdd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 8VDD # _exptl.entry_id 8VDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 109.518 _cell.angle_gamma 90 _cell.entry_id 8VDD _cell.length_a 158.833 _cell.length_b 40.698 _cell.length_c 92.604 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 E _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 75 A CYS 73 1_555 C SG CYS 14 C CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 110 A CYS 108 1_555 A SG CYS 166 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 15 B CYS 15 1_555 B SG CYS 79 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 117 B CYS 117 1_555 B SG CYS 173 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 121 A ASN 119 1_555 D C1 NAG . A NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 8VDD _atom_sites.fract_transf_matrix[1][1] 0.006296 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002232 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024571 _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] 0.011457 _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 NAG A 1 201 202 NAG NAG . E 5 GOL C 1 201 201 GOL GOL . F 6 HOH A 1 301 36 HOH HOH . F 6 HOH A 2 302 33 HOH HOH . F 6 HOH A 3 303 34 HOH HOH . F 6 HOH A 4 304 45 HOH HOH . F 6 HOH A 5 305 8 HOH HOH . F 6 HOH A 6 306 37 HOH HOH . F 6 HOH A 7 307 40 HOH HOH . F 6 HOH A 8 308 38 HOH HOH . F 6 HOH A 9 309 12 HOH HOH . F 6 HOH A 10 310 55 HOH HOH . F 6 HOH A 11 311 14 HOH HOH . F 6 HOH A 12 312 30 HOH HOH . F 6 HOH A 13 313 10 HOH HOH . F 6 HOH A 14 314 7 HOH HOH . F 6 HOH A 15 315 32 HOH HOH . F 6 HOH A 16 316 35 HOH HOH . F 6 HOH A 17 317 39 HOH HOH . F 6 HOH A 18 318 5 HOH HOH . F 6 HOH A 19 319 16 HOH HOH . F 6 HOH A 20 320 43 HOH HOH . F 6 HOH A 21 321 51 HOH HOH . F 6 HOH A 22 322 13 HOH HOH . F 6 HOH A 23 323 44 HOH HOH . G 6 HOH B 1 201 25 HOH HOH . G 6 HOH B 2 202 17 HOH HOH . G 6 HOH B 3 203 21 HOH HOH . G 6 HOH B 4 204 23 HOH HOH . G 6 HOH B 5 205 41 HOH HOH . G 6 HOH B 6 206 20 HOH HOH . G 6 HOH B 7 207 52 HOH HOH . G 6 HOH B 8 208 47 HOH HOH . G 6 HOH B 9 209 49 HOH HOH . G 6 HOH B 10 210 9 HOH HOH . G 6 HOH B 11 211 24 HOH HOH . G 6 HOH B 12 212 28 HOH HOH . G 6 HOH B 13 213 27 HOH HOH . G 6 HOH B 14 214 48 HOH HOH . G 6 HOH B 15 215 11 HOH HOH . G 6 HOH B 16 216 18 HOH HOH . G 6 HOH B 17 217 22 HOH HOH . G 6 HOH B 18 218 26 HOH HOH . G 6 HOH B 19 219 50 HOH HOH . G 6 HOH B 20 220 31 HOH HOH . G 6 HOH B 21 221 4 HOH HOH . G 6 HOH B 22 222 42 HOH HOH . G 6 HOH B 23 223 56 HOH HOH . G 6 HOH B 24 224 46 HOH HOH . G 6 HOH B 25 225 54 HOH HOH . G 6 HOH B 26 226 53 HOH HOH . H 6 HOH C 1 301 1 HOH HOH . H 6 HOH C 2 302 29 HOH HOH . H 6 HOH C 3 303 19 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 GOL . . . E 5 26.775 -19.572 41.484 1 43.66 ? C1 GOL 201 C 1 HETATM 2 O O1 GOL . . . E 5 26.481 -18.372 40.826 1 50.15 ? O1 GOL 201 C 1 HETATM 3 C C2 GOL . . . E 5 27.726 -20.369 40.557 1 51.84 ? C2 GOL 201 C 1 HETATM 4 O O2 GOL . . . E 5 27.907 -21.677 40.992 1 56.87 ? O2 GOL 201 C 1 HETATM 5 C C3 GOL . . . E 5 29.049 -19.558 40.543 1 47.28 ? C3 GOL 201 C 1 HETATM 6 O O3 GOL . . . E 5 29.063 -18.797 39.371 1 39.41 ? O3 GOL 201 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 6 #