data_3PVB # _model_server_result.job_id 3aK09H9Z-Wg63JonQHZCsg _model_server_result.datetime_utc '2024-11-24 22:02:30' _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 3pvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1}' # _entry.id 3PVB # _exptl.entry_id 3PVB _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 90 _cell.angle_gamma 120 _cell.entry_id 3PVB _cell.length_a 116.667 _cell.length_b 116.667 _cell.length_c 140.103 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PVB _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 covale ? covale1 A C GLY 4 A GLY 9 1_555 A N SEP 5 A SEP 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C SEP 5 A SEP 10 1_555 A N GLU 6 A GLU 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C PHE 133 A PHE 138 1_555 A N SEP 134 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale4 A C SEP 134 A SEP 139 1_555 A N GLU 135 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C TRP 191 A TRP 196 1_555 A N TPO 192 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale6 A C TPO 192 A TPO 197 1_555 A N LEU 193 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C VAL 332 A VAL 337 1_555 A N SEP 333 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 A C SEP 333 A SEP 338 1_555 A N ILE 334 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A OD1 ASN 166 A ASN 171 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc2 A OD1 ASP 179 A ASP 184 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc3 A OD2 ASP 179 A ASP 184 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc4 C N3B ANP . A ANP 400 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 C O2A ANP . A ANP 400 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc6 C O2G ANP . A ANP 400 1_555 D MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc7 C O1G ANP . A ANP 400 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? # _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 179 n n C1 C2 GOL sing 180 n n C1 H11 GOL sing 181 n n C1 H12 GOL sing 182 n n O1 HO1 GOL sing 183 n n C2 O2 GOL sing 184 n n C2 C3 GOL sing 185 n n C2 H2 GOL sing 186 n n O2 HO2 GOL sing 187 n n C3 O3 GOL sing 188 n n C3 H31 GOL sing 189 n n C3 H32 GOL sing 190 n n O3 HO3 GOL sing 191 n n # _atom_sites.entry_id 3PVB _atom_sites.fract_transf_matrix[1][1] 0.008571 _atom_sites.fract_transf_matrix[1][2] 0.004949 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009897 _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] 0.007138 _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 ANP A 1 400 400 ANP ANP . D 4 MN A 1 401 401 MN MN . E 4 MN A 1 402 402 MN MN . F 5 GOL B 1 1 1 GOL GOL . G 6 HOH A 1 2 2 HOH WAT . G 6 HOH A 2 3 3 HOH WAT . G 6 HOH A 3 4 4 HOH WAT . G 6 HOH A 4 5 5 HOH WAT . G 6 HOH A 5 351 6 HOH WAT . G 6 HOH A 6 352 7 HOH WAT . G 6 HOH A 7 353 8 HOH WAT . G 6 HOH A 8 354 9 HOH WAT . G 6 HOH A 9 355 10 HOH WAT . G 6 HOH A 10 356 11 HOH WAT . G 6 HOH A 11 357 12 HOH WAT . G 6 HOH A 12 358 13 HOH WAT . G 6 HOH A 13 359 15 HOH WAT . H 6 HOH B 1 14 14 HOH WAT . H 6 HOH B 2 16 16 HOH WAT . # 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 . . . F 5 75.545 46.358 51.696 1 56.13 ? C1 GOL 1 B 1 HETATM 2 O O1 GOL . . . F 5 76.96 45.782 52.203 1 54.75 ? O1 GOL 1 B 1 HETATM 3 C C2 GOL . . . F 5 75.188 46.648 50.369 1 56.25 ? C2 GOL 1 B 1 HETATM 4 O O2 GOL . . . F 5 75.263 47.971 50.113 1 57.42 ? O2 GOL 1 B 1 HETATM 5 C C3 GOL . . . F 5 74.892 45.625 49.792 1 55.28 ? C3 GOL 1 B 1 HETATM 6 O O3 GOL . . . F 5 74.628 44.113 49.53 1 54.73 ? O3 GOL 1 B 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 444 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #