data_4KWE # _model_server_result.job_id '_Jwl2qK4UJglSE0TgUNF0g' _model_server_result.datetime_utc '2024-11-15 06:55:43' _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 4kwe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1000}' # _entry.id 4KWE # _exptl.entry_id 4KWE _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 3 _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 4KWE _cell.length_a 132.509 _cell.length_b 132.509 _cell.length_c 321.549 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KWE _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # 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 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D 1 1 B,E 2 1 C,F 3 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 D N N ? 2 E N N ? 2 F 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 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 4KWE _atom_sites.fract_transf_matrix[1][1] 0.007547 _atom_sites.fract_transf_matrix[1][2] 0.004357 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008714 _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] 0.00311 _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 2 GDP A 1 1000 1000 GDP GDP . E 2 GDP B 1 1000 1000 GDP GDP . F 2 GDP C 1 1000 1000 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 46.607 -11.981 -18.389 1 112.59 ? PB GDP 1000 A 1 HETATM 2 O O1B GDP . . . D 2 46.364 -13.252 -19.185 1 111.09 ? O1B GDP 1000 A 1 HETATM 3 O O2B GDP . . . D 2 47.62 -11.112 -19.079 1 112.45 ? O2B GDP 1000 A 1 HETATM 4 O O3B GDP . . . D 2 45.314 -11.217 -18.199 1 113.6 ? O3B GDP 1000 A 1 HETATM 5 O O3A GDP . . . D 2 47.193 -12.354 -16.936 1 111.9 ? O3A GDP 1000 A 1 HETATM 6 P PA GDP . . . D 2 48.559 -13.187 -16.748 1 109.9 ? PA GDP 1000 A 1 HETATM 7 O O1A GDP . . . D 2 48.98 -13.85 -18.039 1 109.13 ? O1A GDP 1000 A 1 HETATM 8 O O2A GDP . . . D 2 49.669 -12.333 -16.176 1 110.83 ? O2A GDP 1000 A 1 HETATM 9 O O5' GDP . . . D 2 48.121 -14.26 -15.66 1 109.18 ? O5' GDP 1000 A 1 HETATM 10 C C5' GDP . . . D 2 47.392 -15.419 -16.03 1 108.04 ? C5' GDP 1000 A 1 HETATM 11 C C4' GDP . . . D 2 48.058 -16.638 -15.409 1 107.27 ? C4' GDP 1000 A 1 HETATM 12 O O4' GDP . . . D 2 49.405 -16.743 -15.867 1 106.85 ? O4' GDP 1000 A 1 HETATM 13 C C3' GDP . . . D 2 48.158 -16.542 -13.898 1 108.23 ? C3' GDP 1000 A 1 HETATM 14 O O3' GDP . . . D 2 46.991 -17.076 -13.265 1 108.71 ? O3' GDP 1000 A 1 HETATM 15 C C2' GDP . . . D 2 49.426 -17.313 -13.572 1 108 ? C2' GDP 1000 A 1 HETATM 16 O O2' GDP . . . D 2 49.166 -18.694 -13.289 1 107.54 ? O2' GDP 1000 A 1 HETATM 17 C C1' GDP . . . D 2 50.258 -17.238 -14.837 1 107.36 ? C1' GDP 1000 A 1 HETATM 18 N N9 GDP . . . D 2 51.427 -16.339 -14.665 1 108.14 ? N9 GDP 1000 A 1 HETATM 19 C C8 GDP . . . D 2 51.472 -15.193 -13.959 1 109.48 ? C8 GDP 1000 A 1 HETATM 20 N N7 GDP . . . D 2 52.704 -14.625 -14.013 1 110.37 ? N7 GDP 1000 A 1 HETATM 21 C C5 GDP . . . D 2 53.48 -15.421 -14.771 1 109.54 ? C5 GDP 1000 A 1 HETATM 22 C C6 GDP . . . D 2 54.889 -15.415 -15.239 1 110.16 ? C6 GDP 1000 A 1 HETATM 23 O O6 GDP . . . D 2 55.672 -14.491 -14.923 1 111.53 ? O6 GDP 1000 A 1 HETATM 24 N N1 GDP . . . D 2 55.299 -16.432 -16.017 1 109.21 ? N1 GDP 1000 A 1 HETATM 25 C C2 GDP . . . D 2 54.482 -17.445 -16.382 1 107.85 ? C2 GDP 1000 A 1 HETATM 26 N N2 GDP . . . D 2 54.979 -18.437 -17.167 1 107.03 ? N2 GDP 1000 A 1 HETATM 27 N N3 GDP . . . D 2 53.181 -17.508 -15.988 1 107.49 ? N3 GDP 1000 A 1 HETATM 28 C C4 GDP . . . D 2 52.633 -16.547 -15.2 1 108.12 ? C4 GDP 1000 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #