data_4ZDW # _model_server_result.job_id qxv3d-PO5m942dOI3-obPQ _model_server_result.datetime_utc '2025-06-29 22:35:14' _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 4zdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 4ZDW # _exptl.entry_id 4ZDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 4ZDW _cell.length_a 116.9 _cell.length_b 119.28 _cell.length_c 122.86 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 4ZDW _atom_sites.fract_transf_matrix[1][1] 0.008554 _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] 0.008384 _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] 0.008139 _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 D 3 GDP A 1 201 201 GDP GDP . E 4 HOH A 1 301 13 HOH HOH . E 4 HOH A 2 302 42 HOH HOH . E 4 HOH A 3 303 21 HOH HOH . E 4 HOH A 4 304 32 HOH HOH . E 4 HOH A 5 305 9 HOH HOH . E 4 HOH A 6 306 41 HOH HOH . E 4 HOH A 7 307 17 HOH HOH . E 4 HOH A 8 308 44 HOH HOH . E 4 HOH A 9 309 3 HOH HOH . E 4 HOH A 10 310 15 HOH HOH . F 4 HOH B 1 201 11 HOH HOH . F 4 HOH B 2 202 1 HOH HOH . F 4 HOH B 3 203 30 HOH HOH . F 4 HOH B 4 204 22 HOH HOH . F 4 HOH B 5 205 46 HOH HOH . F 4 HOH B 6 206 45 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 P PB GDP . . . D 3 -27.49 -12.824 -16.566 1 68.11 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . D 3 -26.294 -13.697 -16.896 1 59.97 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . D 3 -28.771 -13.62 -16.475 1 62.96 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . D 3 -27.206 -11.878 -15.412 1 66.08 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . D 3 -27.815 -11.807 -17.794 1 67.05 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . D 3 -29.293 -11.243 -18.224 1 74.3 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . D 3 -30.106 -12.324 -18.928 1 63.73 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . D 3 -29.934 -10.389 -17.142 1 65.12 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . D 3 -28.818 -10.236 -19.38 1 75.07 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . D 3 -28.351 -8.908 -19.126 1 78.57 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . D 3 -28.678 -8.033 -20.344 1 82.46 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . D 3 -28.312 -8.654 -21.599 1 79.11 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . D 3 -30.172 -7.745 -20.416 1 79.45 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . D 3 -30.344 -6.34 -20.677 1 72.64 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . D 3 -30.655 -8.656 -21.542 1 74.67 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . D 3 -31.842 -8.168 -22.168 1 71.63 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . D 3 -29.447 -8.718 -22.472 1 74.93 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . D 3 -29.385 -9.93 -23.34 1 79.08 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . D 3 -29.523 -11.227 -22.988 1 77.73 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . D 3 -29.392 -12.061 -24.063 1 75.63 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . D 3 -29.164 -11.299 -25.153 1 77.88 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . D 3 -28.93 -11.514 -26.615 1 75.54 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . D 3 -28.922 -12.652 -27.14 1 70.03 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . D 3 -28.728 -10.418 -27.373 1 79.89 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . D 3 -28.729 -9.154 -26.863 1 81.85 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . D 3 -28.521 -8.093 -27.678 1 81.42 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . D 3 -28.935 -8.886 -25.547 1 81.79 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . D 3 -29.157 -9.896 -24.66 1 81.89 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #