data_3WGK # _model_server_result.job_id tt-ElmhR9XHYsBHv6r6T7w _model_server_result.datetime_utc '2024-11-05 01:16:03' _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 3wgk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 3WGK # _exptl.entry_id 3WGK _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.87 _cell.angle_gamma 90 _cell.entry_id 3WGK _cell.length_a 44.335 _cell.length_b 95.927 _cell.length_c 72.136 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WGK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C 1 1 B,D 2 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 C N N ? 2 D N 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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 3WGK _atom_sites.fract_transf_matrix[1][1] 0.022556 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00433 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010425 _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] 0.014116 _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 C 2 GDP A 1 400 400 GDP GDP . D 2 GDP B 1 400 400 GDP GDP . # 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 2 21.089 3.628 3.829 1 76.88 ? PB GDP 400 B 1 HETATM 2 O O1B GDP . . . D 2 21.074 5.104 4.082 1 63.93 ? O1B GDP 400 B 1 HETATM 3 O O2B GDP . . . D 2 20.145 2.961 4.783 1 63.5 ? O2B GDP 400 B 1 HETATM 4 O O3B GDP . . . D 2 22.466 3.074 4.052 1 68.88 ? O3B GDP 400 B 1 HETATM 5 O O3A GDP . . . D 2 20.492 3.377 2.361 1 79.05 ? O3A GDP 400 B 1 HETATM 6 P PA GDP . . . D 2 21.234 2.613 1.164 1 74.17 ? PA GDP 400 B 1 HETATM 7 O O1A GDP . . . D 2 21.216 3.47 -0.073 1 76.4 ? O1A GDP 400 B 1 HETATM 8 O O2A GDP . . . D 2 22.632 2.164 1.486 1 78.76 ? O2A GDP 400 B 1 HETATM 9 O O5' GDP . . . D 2 20.297 1.338 0.965 1 71.52 ? O5' GDP 400 B 1 HETATM 10 C C5' GDP . . . D 2 20.808 0.068 1.338 1 64.23 ? C5' GDP 400 B 1 HETATM 11 C C4' GDP . . . D 2 20.313 -0.957 0.343 1 64 ? C4' GDP 400 B 1 HETATM 12 O O4' GDP . . . D 2 19.327 -0.344 -0.483 1 66.33 ? O4' GDP 400 B 1 HETATM 13 C C3' GDP . . . D 2 21.435 -1.396 -0.574 1 57.22 ? C3' GDP 400 B 1 HETATM 14 O O3' GDP . . . D 2 22.022 -2.624 -0.123 1 61.31 ? O3' GDP 400 B 1 HETATM 15 C C2' GDP . . . D 2 20.763 -1.533 -1.928 1 60.28 ? C2' GDP 400 B 1 HETATM 16 O O2' GDP . . . D 2 20.424 -2.901 -2.163 1 59.56 ? O2' GDP 400 B 1 HETATM 17 C C1' GDP . . . D 2 19.479 -0.729 -1.849 1 60.08 ? C1' GDP 400 B 1 HETATM 18 N N9 GDP . . . D 2 19.592 0.496 -2.684 1 64.08 ? N9 GDP 400 B 1 HETATM 19 C C8 GDP . . . D 2 20.71 1.232 -2.853 1 66.59 ? C8 GDP 400 B 1 HETATM 20 N N7 GDP . . . D 2 20.486 2.301 -3.66 1 59.14 ? N7 GDP 400 B 1 HETATM 21 C C5 GDP . . . D 2 19.191 2.272 -4.02 1 63.18 ? C5 GDP 400 B 1 HETATM 22 C C6 GDP . . . D 2 18.312 3.117 -4.86 1 61.49 ? C6 GDP 400 B 1 HETATM 23 O O6 GDP . . . D 2 18.745 4.137 -5.435 1 65.87 ? O6 GDP 400 B 1 HETATM 24 N N1 GDP . . . D 2 17.036 2.757 -4.977 1 61.47 ? N1 GDP 400 B 1 HETATM 25 C C2 GDP . . . D 2 16.543 1.663 -4.37 1 64.45 ? C2 GDP 400 B 1 HETATM 26 N N2 GDP . . . D 2 15.227 1.383 -4.56 1 65.97 ? N2 GDP 400 B 1 HETATM 27 N N3 GDP . . . D 2 17.292 0.836 -3.584 1 65.85 ? N3 GDP 400 B 1 HETATM 28 C C4 GDP . . . D 2 18.604 1.086 -3.372 1 65.42 ? C4 GDP 400 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #