data_8VWN # _model_server_result.job_id NQ_vw35eHReg-UYzPw6Bow _model_server_result.datetime_utc '2024-11-28 05:32:57' _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":"J","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 . . . J 2 68.75 -45.721 -29.334 1 170.11 ? PB GDP 301 D 1 HETATM 2 O O1B GDP . . . J 2 67.636 -44.735 -29.08 1 158.89 ? O1B GDP 301 D 1 HETATM 3 O O2B GDP . . . J 2 68.273 -47.083 -29.777 1 172.76 ? O2B GDP 301 D 1 HETATM 4 O O3B GDP . . . J 2 69.817 -45.774 -28.266 1 162.31 ? O3B GDP 301 D 1 HETATM 5 O O3A GDP . . . J 2 69.493 -45.123 -30.636 1 169.99 ? O3A GDP 301 D 1 HETATM 6 P PA GDP . . . J 2 70.402 -43.79 -30.599 1 160.11 ? PA GDP 301 D 1 HETATM 7 O O1A GDP . . . J 2 69.619 -42.665 -29.973 1 153.96 ? O1A GDP 301 D 1 HETATM 8 O O2A GDP . . . J 2 71.765 -44.148 -30.057 1 163.12 ? O2A GDP 301 D 1 HETATM 9 O O5' GDP . . . J 2 70.564 -43.469 -32.166 1 168.1 ? O5' GDP 301 D 1 HETATM 10 C C5' GDP . . . J 2 71.652 -42.684 -32.645 1 175.44 ? C5' GDP 301 D 1 HETATM 11 C C4' GDP . . . J 2 71.494 -42.498 -34.148 1 180.26 ? C4' GDP 301 D 1 HETATM 12 O O4' GDP . . . J 2 70.328 -41.713 -34.404 1 179.27 ? O4' GDP 301 D 1 HETATM 13 C C3' GDP . . . J 2 72.678 -41.759 -34.752 1 189.14 ? C3' GDP 301 D 1 HETATM 14 O O3' GDP . . . J 2 73.514 -42.661 -35.484 1 192.77 ? O3' GDP 301 D 1 HETATM 15 C C2' GDP . . . J 2 72.081 -40.724 -35.683 1 187.56 ? C2' GDP 301 D 1 HETATM 16 O O2' GDP . . . J 2 72.289 -41.113 -37.043 1 195.68 ? O2' GDP 301 D 1 HETATM 17 C C1' GDP . . . J 2 70.592 -40.703 -35.381 1 182.25 ? C1' GDP 301 D 1 HETATM 18 N N9 GDP . . . J 2 70.234 -39.377 -34.825 1 179.87 ? N9 GDP 301 D 1 HETATM 19 C C8 GDP . . . J 2 70.286 -39.043 -33.521 1 176.69 ? C8 GDP 301 D 1 HETATM 20 N N7 GDP . . . J 2 69.901 -37.756 -33.331 1 174.35 ? N7 GDP 301 D 1 HETATM 21 C C5 GDP . . . J 2 69.596 -37.245 -34.537 1 177.56 ? C5 GDP 301 D 1 HETATM 22 C C6 GDP . . . J 2 69.121 -35.94 -35.052 1 177.12 ? C6 GDP 301 D 1 HETATM 23 O O6 GDP . . . J 2 68.913 -34.984 -34.279 1 173.63 ? O6 GDP 301 D 1 HETATM 24 N N1 GDP . . . J 2 68.925 -35.811 -36.369 1 179.64 ? N1 GDP 301 D 1 HETATM 25 C C2 GDP . . . J 2 69.144 -36.824 -37.228 1 183.16 ? C2 GDP 301 D 1 HETATM 26 N N2 GDP . . . J 2 68.919 -36.606 -38.547 1 182.89 ? N2 GDP 301 D 1 HETATM 27 N N3 GDP . . . J 2 69.579 -38.05 -36.828 1 183.79 ? N3 GDP 301 D 1 HETATM 28 C C4 GDP . . . J 2 69.818 -38.315 -35.52 1 181.09 ? C4 GDP 301 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #