data_3DV3 # _model_server_result.job_id 4G83kAohtpWBPaqgotIWjA _model_server_result.datetime_utc '2024-11-07 10:05:37' _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 3dv3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":9003}' # _entry.id 3DV3 # _exptl.entry_id 3DV3 _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 3DV3 _cell.length_a 81.596 _cell.length_b 81.596 _cell.length_c 129.966 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DV3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1,2 A,B,C,D,E,F 2 1 # 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' 4_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 81.596 0 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 metalc ? metalc1 B MG MG . A MG 1 1_555 A OD1 ASN 135 A ASN 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc2 B MG MG . A MG 1 1_555 A OD2 ASP 148 A ASP 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc3 B MG MG . A MG 1 1_555 C O1B ATP . A ATP 9000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? metalc ? metalc4 B MG MG . A MG 1 1_555 C O2A ATP . A ATP 9000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc5 B MG MG . A MG 1 1_555 F O HOH . A HOH 9020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B MG MG . A MG 1 1_555 F O HOH . A HOH 9078 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? # _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 178 n n C1 C2 GOL sing 179 n n C1 H11 GOL sing 180 n n C1 H12 GOL sing 181 n n O1 HO1 GOL sing 182 n n C2 O2 GOL sing 183 n n C2 C3 GOL sing 184 n n C2 H2 GOL sing 185 n n O2 HO2 GOL sing 186 n n C3 O3 GOL sing 187 n n C3 H31 GOL sing 188 n n C3 H32 GOL sing 189 n n O3 HO3 GOL sing 190 n n # _atom_sites.entry_id 3DV3 _atom_sites.fract_transf_matrix[1][1] 0.012256 _atom_sites.fract_transf_matrix[1][2] 0.007076 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014151 _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] 0.007694 _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 B 2 MG A 1 1 1 MG MG . C 3 ATP A 1 9000 9000 ATP ATP . D 4 MEK A 1 9001 1 MEK MEK . E 5 GOL A 1 9003 9003 GOL GOL . F 6 HOH A 1 9004 1 HOH HOH . F 6 HOH A 2 9005 2 HOH HOH . F 6 HOH A 3 9006 3 HOH HOH . F 6 HOH A 4 9007 4 HOH HOH . F 6 HOH A 5 9008 5 HOH HOH . F 6 HOH A 6 9009 6 HOH HOH . F 6 HOH A 7 9010 7 HOH HOH . F 6 HOH A 8 9011 8 HOH HOH . F 6 HOH A 9 9012 9 HOH HOH . F 6 HOH A 10 9013 10 HOH HOH . F 6 HOH A 11 9014 11 HOH HOH . F 6 HOH A 12 9015 12 HOH HOH . F 6 HOH A 13 9016 13 HOH HOH . F 6 HOH A 14 9017 14 HOH HOH . F 6 HOH A 15 9018 15 HOH HOH . F 6 HOH A 16 9019 16 HOH HOH . F 6 HOH A 17 9020 17 HOH HOH . F 6 HOH A 18 9021 18 HOH HOH . F 6 HOH A 19 9022 19 HOH HOH . F 6 HOH A 20 9023 20 HOH HOH . F 6 HOH A 21 9024 21 HOH HOH . F 6 HOH A 22 9025 22 HOH HOH . F 6 HOH A 23 9026 23 HOH HOH . F 6 HOH A 24 9027 24 HOH HOH . F 6 HOH A 25 9028 25 HOH HOH . F 6 HOH A 26 9029 27 HOH HOH . F 6 HOH A 27 9030 28 HOH HOH . F 6 HOH A 28 9031 31 HOH HOH . F 6 HOH A 29 9032 32 HOH HOH . F 6 HOH A 30 9033 33 HOH HOH . F 6 HOH A 31 9034 34 HOH HOH . F 6 HOH A 32 9035 35 HOH HOH . F 6 HOH A 33 9036 36 HOH HOH . F 6 HOH A 34 9037 37 HOH HOH . F 6 HOH A 35 9038 38 HOH HOH . F 6 HOH A 36 9039 39 HOH HOH . F 6 HOH A 37 9040 40 HOH HOH . F 6 HOH A 38 9041 41 HOH HOH . F 6 HOH A 39 9042 42 HOH HOH . F 6 HOH A 40 9043 44 HOH HOH . F 6 HOH A 41 9044 45 HOH HOH . F 6 HOH A 42 9045 46 HOH HOH . F 6 HOH A 43 9046 47 HOH HOH . F 6 HOH A 44 9047 48 HOH HOH . F 6 HOH A 45 9048 49 HOH HOH . F 6 HOH A 46 9049 50 HOH HOH . F 6 HOH A 47 9050 51 HOH HOH . F 6 HOH A 48 9051 52 HOH HOH . F 6 HOH A 49 9052 53 HOH HOH . F 6 HOH A 50 9053 54 HOH HOH . F 6 HOH A 51 9054 55 HOH HOH . F 6 HOH A 52 9055 56 HOH HOH . F 6 HOH A 53 9056 57 HOH HOH . F 6 HOH A 54 9057 59 HOH HOH . F 6 HOH A 55 9058 60 HOH HOH . F 6 HOH A 56 9059 61 HOH HOH . F 6 HOH A 57 9060 62 HOH HOH . F 6 HOH A 58 9061 65 HOH HOH . F 6 HOH A 59 9062 66 HOH HOH . F 6 HOH A 60 9063 67 HOH HOH . F 6 HOH A 61 9064 69 HOH HOH . F 6 HOH A 62 9065 70 HOH HOH . F 6 HOH A 63 9066 71 HOH HOH . F 6 HOH A 64 9067 73 HOH HOH . F 6 HOH A 65 9068 74 HOH HOH . F 6 HOH A 66 9069 75 HOH HOH . F 6 HOH A 67 9070 76 HOH HOH . F 6 HOH A 68 9071 77 HOH HOH . F 6 HOH A 69 9072 78 HOH HOH . F 6 HOH A 70 9073 79 HOH HOH . F 6 HOH A 71 9074 80 HOH HOH . F 6 HOH A 72 9075 81 HOH HOH . F 6 HOH A 73 9076 82 HOH HOH . F 6 HOH A 74 9077 83 HOH HOH . F 6 HOH A 75 9078 84 HOH HOH . F 6 HOH A 76 9079 85 HOH HOH . F 6 HOH A 77 9080 86 HOH HOH . F 6 HOH A 78 9081 87 HOH HOH . F 6 HOH A 79 9082 88 HOH HOH . F 6 HOH A 80 9083 89 HOH HOH . F 6 HOH A 81 9084 90 HOH HOH . F 6 HOH A 82 9085 91 HOH HOH . F 6 HOH A 83 9086 92 HOH HOH . F 6 HOH A 84 9087 93 HOH HOH . F 6 HOH A 85 9088 94 HOH HOH . F 6 HOH A 86 9089 95 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 35.115 -19.843 14.334 1 69.11 ? C1 GOL 9003 A 1 HETATM 2 O O1 GOL . . . E 5 34.232 -19.373 15.327 1 66.43 ? O1 GOL 9003 A 1 HETATM 3 C C2 GOL . . . E 5 34.573 -21.08 13.602 1 72.11 ? C2 GOL 9003 A 1 HETATM 4 O O2 GOL . . . E 5 33.664 -21.85 14.35 1 75.56 ? O2 GOL 9003 A 1 HETATM 5 C C3 GOL . . . E 5 33.762 -20.587 12.431 1 68.07 ? C3 GOL 9003 A 1 HETATM 6 O O3 GOL . . . E 5 34.684 -20.05 11.518 1 68.81 ? O3 GOL 9003 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #