data_8VWN # _model_server_result.job_id bLaWoJDm1GZdS4tnRt0euQ _model_server_result.datetime_utc '2024-11-28 05:35:34' _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 8vwn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 8VWN # _exptl.entry_id 8VWN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.88 _cell.angle_gamma 90 _cell.entry_id 8VWN _cell.length_a 194.27 _cell.length_b 155.309 _cell.length_c 50.916 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VWN _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' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,L 1 1 B,G,H,M 2 1 C,I 3 1 D,J,K,N 4 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 ? 2 E N N ? 2 G N N ? 2 I N N ? 2 J 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 metalc ? metalc1 F MG MG . A MG 302 1_555 L O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc2 F MG MG . A MG 302 1_555 L O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc3 F MG MG . A MG 302 1_555 L O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc4 F MG MG . A MG 302 1_555 L O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc5 F MG MG . A MG 302 1_555 L O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc6 F MG MG . A MG 302 1_555 L O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc7 H MG MG . B MG 302 1_555 M O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc8 H MG MG . B MG 302 1_555 M O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc9 H MG MG . B MG 302 1_555 M O HOH . B HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 H MG MG . B MG 302 1_555 M O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc11 H MG MG . B MG 302 1_555 M O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc12 H MG MG . B MG 302 1_555 M O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc13 K MG MG . D MG 302 1_555 N O HOH . D HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc14 K MG MG . D MG 302 1_555 N O HOH . D HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc15 K MG MG . D MG 302 1_555 N O HOH . D HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc16 K MG MG . D MG 302 1_555 N O HOH . D HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc17 K MG MG . D MG 302 1_555 N O HOH . D HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc18 K MG MG . D MG 302 1_555 N O HOH . D HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 8VWN _atom_sites.fract_transf_matrix[1][1] 0.005147 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00053 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006439 _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] 0.019744 _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 E 2 GDP A 1 301 1 GDP GDP . F 3 MG A 1 302 1 MG MO6 . G 2 GDP B 1 301 2 GDP GDP . H 3 MG B 1 302 2 MG MO6 . I 2 GDP C 1 301 3 GDP GDP . J 2 GDP D 1 301 4 GDP GDP . K 3 MG D 1 302 3 MG MO6 . L 4 HOH A 1 401 1 HOH MO6 . L 4 HOH A 2 402 1 HOH MO6 . L 4 HOH A 3 403 1 HOH MO6 . L 4 HOH A 4 404 1 HOH MO6 . L 4 HOH A 5 405 1 HOH MO6 . L 4 HOH A 6 406 1 HOH MO6 . M 4 HOH B 1 401 2 HOH MO6 . M 4 HOH B 2 402 2 HOH MO6 . M 4 HOH B 3 403 2 HOH MO6 . M 4 HOH B 4 404 2 HOH MO6 . M 4 HOH B 5 405 2 HOH MO6 . M 4 HOH B 6 406 2 HOH MO6 . M 4 HOH B 7 407 1 HOH HOH . N 4 HOH D 1 401 3 HOH MO6 . N 4 HOH D 2 402 3 HOH MO6 . N 4 HOH D 3 403 3 HOH MO6 . N 4 HOH D 4 404 3 HOH MO6 . N 4 HOH D 5 405 3 HOH MO6 . N 4 HOH D 6 406 3 HOH MO6 . # 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 P PB GDP . . . E 2 20.163 -5.941 -39.18 1 147.43 ? PB GDP 301 A 1 HETATM 2 O O1B GDP . . . E 2 18.903 -6.183 -39.976 1 150.97 ? O1B GDP 301 A 1 HETATM 3 O O2B GDP . . . E 2 20.877 -7.203 -38.754 1 141.83 ? O2B GDP 301 A 1 HETATM 4 O O3B GDP . . . E 2 19.978 -4.914 -38.089 1 138.3 ? O3B GDP 301 A 1 HETATM 5 O O3A GDP . . . E 2 21.171 -5.218 -40.215 1 138.87 ? O3A GDP 301 A 1 HETATM 6 P PA GDP . . . E 2 21.5 -5.815 -41.679 1 133.29 ? PA GDP 301 A 1 HETATM 7 O O1A GDP . . . E 2 20.431 -6.795 -42.1 1 137.27 ? O1A GDP 301 A 1 HETATM 8 O O2A GDP . . . E 2 22.943 -6.259 -41.68 1 136.12 ? O2A GDP 301 A 1 HETATM 9 O O5' GDP . . . E 2 21.39 -4.525 -42.634 1 140.66 ? O5' GDP 301 A 1 HETATM 10 C C5' GDP . . . E 2 20.435 -4.566 -43.691 1 146.49 ? C5' GDP 301 A 1 HETATM 11 C C4' GDP . . . E 2 20.782 -3.621 -44.835 1 148.37 ? C4' GDP 301 A 1 HETATM 12 O O4' GDP . . . E 2 21.24 -2.346 -44.38 1 143.26 ? O4' GDP 301 A 1 HETATM 13 C C3' GDP . . . E 2 21.891 -4.162 -45.725 1 153.53 ? C3' GDP 301 A 1 HETATM 14 O O3' GDP . . . E 2 21.344 -4.882 -46.834 1 152.44 ? O3' GDP 301 A 1 HETATM 15 C C2' GDP . . . E 2 22.619 -2.927 -46.212 1 162.29 ? C2' GDP 301 A 1 HETATM 16 O O2' GDP . . . E 2 22.376 -2.757 -47.611 1 173.59 ? O2' GDP 301 A 1 HETATM 17 C C1' GDP . . . E 2 22.009 -1.766 -45.438 1 153.54 ? C1' GDP 301 A 1 HETATM 18 N N9 GDP . . . E 2 23.074 -0.865 -44.93 1 153.73 ? N9 GDP 301 A 1 HETATM 19 C C8 GDP . . . E 2 23.844 -1.086 -43.848 1 148.07 ? C8 GDP 301 A 1 HETATM 20 N N7 GDP . . . E 2 24.722 -0.068 -43.661 1 151.32 ? N7 GDP 301 A 1 HETATM 21 C C5 GDP . . . E 2 24.521 0.831 -44.642 1 153.38 ? C5 GDP 301 A 1 HETATM 22 C C6 GDP . . . E 2 25.109 2.133 -45.033 1 152.99 ? C6 GDP 301 A 1 HETATM 23 O O6 GDP . . . E 2 26.035 2.643 -44.368 1 150.78 ? O6 GDP 301 A 1 HETATM 24 N N1 GDP . . . E 2 24.616 2.748 -46.118 1 157.37 ? N1 GDP 301 A 1 HETATM 25 C C2 GDP . . . E 2 23.618 2.221 -46.854 1 161 ? C2 GDP 301 A 1 HETATM 26 N N2 GDP . . . E 2 23.181 2.91 -47.937 1 159.76 ? N2 GDP 301 A 1 HETATM 27 N N3 GDP . . . E 2 23.033 1.029 -46.553 1 162.7 ? N3 GDP 301 A 1 HETATM 28 C C4 GDP . . . E 2 23.435 0.301 -45.479 1 159.11 ? C4 GDP 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #