data_3D3V # _model_server_result.job_id YuXpxV9WynPdn-XTCNSY_g _model_server_result.datetime_utc '2024-11-04 20:11:44' _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 3d3v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":277}' # _entry.id 3D3V # _exptl.entry_id 3D3V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.61 _cell.angle_gamma 90 _cell.entry_id 3D3V _cell.length_a 224.45 _cell.length_b 48.537 _cell.length_c 93.794 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D3V _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 G N N ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K N 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 101 A CYS 101 1_555 A SG CYS 164 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf2 A SG CYS 203 A CYS 203 1_555 A SG CYS 259 A CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 B SG CYS 26 B CYS 25 1_555 B SG CYS 81 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf4 D SG CYS 22 D CYS 22 1_555 D SG CYS 88 D CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 D SG CYS 133 D CYS 139 1_555 D SG CYS 183 D CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf6 E SG CYS 23 E CYS 23 1_555 E SG CYS 91 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf7 E SG CYS 146 E CYS 147 1_555 E SG CYS 211 E CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? covale ? covale1 C C GLY 4 C GLY 4 1_555 C N F2F 5 C F2F 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 C C F2F 5 C F2F 5 1_555 C N PRO 6 C PRO 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? # _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 152 n n C1 C2 GOL sing 153 n n C1 H11 GOL sing 154 n n C1 H12 GOL sing 155 n n O1 HO1 GOL sing 156 n n C2 O2 GOL sing 157 n n C2 C3 GOL sing 158 n n C2 H2 GOL sing 159 n n O2 HO2 GOL sing 160 n n C3 O3 GOL sing 161 n n C3 H31 GOL sing 162 n n C3 H32 GOL sing 163 n n O3 HO3 GOL sing 164 n n # _atom_sites.entry_id 3D3V _atom_sites.fract_transf_matrix[1][1] 0.004455 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000047 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020603 _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] 0.010662 _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 F 6 GOL A 1 276 276 GOL GOL . G 6 GOL A 1 277 277 GOL GOL . H 6 GOL B 1 100 100 GOL GOL . I 6 GOL B 1 101 101 GOL GOL . J 6 GOL E 1 247 246 GOL GOL . K 6 GOL E 1 248 247 GOL GOL . L 7 HOH A 1 278 278 HOH HOH . L 7 HOH A 2 279 279 HOH HOH . L 7 HOH A 3 280 280 HOH HOH . L 7 HOH A 4 281 281 HOH HOH . L 7 HOH A 5 282 282 HOH HOH . L 7 HOH A 6 283 283 HOH HOH . L 7 HOH A 7 284 284 HOH HOH . L 7 HOH A 8 285 285 HOH HOH . L 7 HOH A 9 286 286 HOH HOH . L 7 HOH A 10 287 287 HOH HOH . L 7 HOH A 11 288 288 HOH HOH . L 7 HOH A 12 289 289 HOH HOH . L 7 HOH A 13 290 290 HOH HOH . M 7 HOH B 1 102 102 HOH HOH . M 7 HOH B 2 103 103 HOH HOH . M 7 HOH B 3 104 104 HOH HOH . M 7 HOH B 4 105 105 HOH HOH . M 7 HOH B 5 106 106 HOH HOH . M 7 HOH B 6 107 107 HOH HOH . N 7 HOH D 1 207 207 HOH HOH . N 7 HOH D 2 208 208 HOH HOH . O 7 HOH E 1 249 248 HOH HOH . O 7 HOH E 2 250 249 HOH HOH . O 7 HOH E 3 251 250 HOH HOH . O 7 HOH E 4 252 251 HOH HOH . O 7 HOH E 5 253 252 HOH HOH . O 7 HOH E 6 254 253 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 . . . G 6 18.207 -9.409 8.256 0.67 68.74 ? C1 GOL 277 A 1 HETATM 2 O O1 GOL . . . G 6 19.349 -9.215 9.08 0.67 68.78 ? O1 GOL 277 A 1 HETATM 3 C C2 GOL . . . G 6 18.075 -8.263 7.251 0.67 68.63 ? C2 GOL 277 A 1 HETATM 4 O O2 GOL . . . G 6 18.991 -7.229 7.56 0.67 68.49 ? O2 GOL 277 A 1 HETATM 5 C C3 GOL . . . G 6 18.312 -8.796 5.837 0.67 68.52 ? C3 GOL 277 A 1 HETATM 6 O O3 GOL . . . G 6 18.055 -7.798 4.869 0.67 68.37 ? O3 GOL 277 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #