data_3Q5S # _model_server_result.job_id ATABmpu_vbZJQfTKoximTA _model_server_result.datetime_utc '2024-11-22 14:16:48' _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 3q5s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":3968}' # _entry.id 3Q5S # _exptl.entry_id 3Q5S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _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 90 _cell.entry_id 3Q5S _cell.length_a 106.407 _cell.length_b 106.407 _cell.length_c 145.571 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3Q5S _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 6_555 x,-y,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 0 72.7855 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 'DG-DC PAIR' hydrog1 B N1 DG 1 B DG -12 1_555 B O2 DC 23 B DC 12 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog2 B N1 DA 2 B DA -11 1_555 B N3 DT 22 B DT 11 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DC 3 B DC -10 1_555 B N1 DG 21 B DG 10 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N4 DC 3 B DC -10 1_555 B O6 DG 21 B DG 10 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O2 DC 3 B DC -10 1_555 B N2 DG 21 B DG 10 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 4 B DC -9 1_555 B N1 DG 20 B DG 9 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 4 B DC -9 1_555 B O6 DG 20 B DG 9 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 4 B DC -9 1_555 B N2 DG 20 B DG 9 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 5 B DC -8 1_555 B N1 DG 19 B DG 8 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 5 B DC -8 1_555 B O6 DG 19 B DG 8 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 5 B DC -8 1_555 B N2 DG 19 B DG 8 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DT 6 B DT -7 1_555 B N1 DA 18 B DA 7 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O4 DT 6 B DT -7 1_555 B N6 DA 18 B DA 7 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog14 B N4 DC 7 B DC -6 1_555 B O6 DG 17 B DG 6 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DC 8 B DC -5 1_555 B N1 DG 16 B DG 5 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N4 DC 8 B DC -5 1_555 B O6 DG 16 B DG 5 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O2 DC 8 B DC -5 1_555 B N2 DG 16 B DG 5 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DC 9 B DC -4 1_555 B N1 DG 15 B DG 4 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 DC 9 B DC -4 1_555 B O6 DG 15 B DG 4 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 DC 9 B DC -4 1_555 B N2 DG 15 B DG 4 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DC 10 B DC -3 1_555 B N1 DG 14 B DG 3 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 DC 10 B DC -3 1_555 B O6 DG 14 B DG 3 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 DC 10 B DC -3 1_555 B N2 DG 14 B DG 3 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DT 11 B DT -2 1_555 B N1 DA 13 B DA 2 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O4 DT 11 B DT -2 1_555 B N6 DA 13 B DA 2 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N1 DA 13 B DA 2 1_555 B N3 DT 11 B DT -2 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N6 DA 13 B DA 2 1_555 B O4 DT 11 B DT -2 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N1 DG 14 B DG 3 1_555 B N3 DC 10 B DC -3 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N2 DG 14 B DG 3 1_555 B O2 DC 10 B DC -3 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B O6 DG 14 B DG 3 1_555 B N4 DC 10 B DC -3 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N1 DG 15 B DG 4 1_555 B N3 DC 9 B DC -4 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B N2 DG 15 B DG 4 1_555 B O2 DC 9 B DC -4 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B O6 DG 15 B DG 4 1_555 B N4 DC 9 B DC -4 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B N1 DG 16 B DG 5 1_555 B N3 DC 8 B DC -5 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N2 DG 16 B DG 5 1_555 B O2 DC 8 B DC -5 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B O6 DG 16 B DG 5 1_555 B N4 DC 8 B DC -5 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog37 B N1 DG 17 B DG 6 1_555 B N3 DC 7 B DC -6 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 B N1 DA 18 B DA 7 1_555 B N3 DT 6 B DT -7 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 B N6 DA 18 B DA 7 1_555 B O4 DT 6 B DT -7 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 B N1 DG 19 B DG 8 1_555 B N3 DC 5 B DC -8 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 B N2 DG 19 B DG 8 1_555 B O2 DC 5 B DC -8 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 B O6 DG 19 B DG 8 1_555 B N4 DC 5 B DC -8 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 B N1 DG 20 B DG 9 1_555 B N3 DC 4 B DC -9 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 B N2 DG 20 B DG 9 1_555 B O2 DC 4 B DC -9 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 B O6 DG 20 B DG 9 1_555 B N4 DC 4 B DC -9 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 B N1 DG 21 B DG 10 1_555 B N3 DC 3 B DC -10 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 B N2 DG 21 B DG 10 1_555 B O2 DC 3 B DC -10 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 B O6 DG 21 B DG 10 1_555 B N4 DC 3 B DC -10 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog49 B N3 DT 22 B DT 11 1_555 B N1 DA 2 B DA -11 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog50 B O2 DC 23 B DC 12 1_555 B N1 DG 1 B DG -12 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 303 n n C1 C2 GOL sing 304 n n C1 H11 GOL sing 305 n n C1 H12 GOL sing 306 n n O1 HO1 GOL sing 307 n n C2 O2 GOL sing 308 n n C2 C3 GOL sing 309 n n C2 H2 GOL sing 310 n n O2 HO2 GOL sing 311 n n C3 O3 GOL sing 312 n n C3 H31 GOL sing 313 n n C3 H32 GOL sing 314 n n O3 HO3 GOL sing 315 n n # _atom_sites.entry_id 3Q5S _atom_sites.fract_transf_matrix[1][1] 0.009398 _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] 0.009398 _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] 0.00687 _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 ACH A 1 1289 1289 ACH ACH . D 4 GOL A 1 3968 3968 GOL GOL . E 5 HOH A 1 285 285 HOH HOH . E 5 HOH A 2 286 286 HOH HOH . E 5 HOH A 3 287 287 HOH HOH . E 5 HOH A 4 288 288 HOH HOH . E 5 HOH A 5 289 289 HOH HOH . E 5 HOH A 6 290 290 HOH HOH . E 5 HOH A 7 291 291 HOH HOH . E 5 HOH A 8 292 292 HOH HOH . F 5 HOH B 1 13 13 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 . . . D 4 71.424 28.642 83.571 1 61.71 ? C1 GOL 3968 A 1 HETATM 2 O O1 GOL . . . D 4 72.352 28.798 82.487 1 59.16 ? O1 GOL 3968 A 1 HETATM 3 C C2 GOL . . . D 4 71.037 27.162 83.874 1 63.99 ? C2 GOL 3968 A 1 HETATM 4 O O2 GOL . . . D 4 69.984 27.06 84.828 1 59.53 ? O2 GOL 3968 A 1 HETATM 5 C C3 GOL . . . D 4 70.618 26.372 82.614 1 52.93 ? C3 GOL 3968 A 1 HETATM 6 O O3 GOL . . . D 4 71.568 25.375 82.218 1 31.86 ? O3 GOL 3968 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #