data_4KWE # _model_server_result.job_id z2Hs1fIIa5PS9eVCuE7Utg _model_server_result.datetime_utc '2024-11-15 07:05:08' _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":"E","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 . . . E 2 21.273 -16.797 28.796 1 116.31 ? PB GDP 1000 B 1 HETATM 2 O O1B GDP . . . E 2 21.198 -16.819 27.285 1 114.52 ? O1B GDP 1000 B 1 HETATM 3 O O2B GDP . . . E 2 22.151 -15.668 29.255 1 116.01 ? O2B GDP 1000 B 1 HETATM 4 O O3B GDP . . . E 2 19.884 -16.612 29.353 1 118.06 ? O3B GDP 1000 B 1 HETATM 5 O O3A GDP . . . E 2 21.873 -18.196 29.322 1 115.57 ? O3A GDP 1000 B 1 HETATM 6 P PA GDP . . . E 2 23.347 -18.709 28.926 1 113.26 ? PA GDP 1000 B 1 HETATM 7 O O1A GDP . . . E 2 23.911 -17.968 27.735 1 111.78 ? O1A GDP 1000 B 1 HETATM 8 O O2A GDP . . . E 2 24.296 -18.612 30.099 1 114.28 ? O2A GDP 1000 B 1 HETATM 9 O O5' GDP . . . E 2 23.076 -20.246 28.565 1 112.45 ? O5' GDP 1000 B 1 HETATM 10 C C5' GDP . . . E 2 22.502 -20.614 27.323 1 111.02 ? C5' GDP 1000 B 1 HETATM 11 C C4' GDP . . . E 2 23.312 -21.765 26.744 1 110.06 ? C4' GDP 1000 B 1 HETATM 12 O O4' GDP . . . E 2 24.676 -21.368 26.594 1 109.27 ? O4' GDP 1000 B 1 HETATM 13 C C3' GDP . . . E 2 23.356 -22.982 27.649 1 111.47 ? C3' GDP 1000 B 1 HETATM 14 O O3' GDP . . . E 2 22.28 -23.877 27.361 1 112.25 ? O3' GDP 1000 B 1 HETATM 15 C C2' GDP . . . E 2 24.719 -23.595 27.386 1 110.86 ? C2' GDP 1000 B 1 HETATM 16 O O2' GDP . . . E 2 24.654 -24.625 26.4 1 110.37 ? O2' GDP 1000 B 1 HETATM 17 C C1' GDP . . . E 2 25.564 -22.463 26.829 1 109.65 ? C1' GDP 1000 B 1 HETATM 18 N N9 GDP . . . E 2 26.611 -22.051 27.8 1 110.46 ? N9 GDP 1000 B 1 HETATM 19 C C8 GDP . . . E 2 26.484 -22.02 29.139 1 112.34 ? C8 GDP 1000 B 1 HETATM 20 N N7 GDP . . . E 2 27.627 -21.588 29.734 1 113.09 ? N7 GDP 1000 B 1 HETATM 21 C C5 GDP . . . E 2 28.52 -21.328 28.764 1 111.49 ? C5 GDP 1000 B 1 HETATM 22 C C6 GDP . . . E 2 29.921 -20.837 28.702 1 111.55 ? C6 GDP 1000 B 1 HETATM 23 O O6 GDP . . . E 2 30.57 -20.554 29.732 1 113.02 ? O6 GDP 1000 B 1 HETATM 24 N N1 GDP . . . E 2 30.48 -20.7 27.492 1 110.1 ? N1 GDP 1000 B 1 HETATM 25 C C2 GDP . . . E 2 29.82 -20.987 26.354 1 108.64 ? C2 GDP 1000 B 1 HETATM 26 N N2 GDP . . . E 2 30.479 -20.816 25.183 1 107.31 ? N2 GDP 1000 B 1 HETATM 27 N N3 GDP . . . E 2 28.534 -21.445 26.337 1 108.72 ? N3 GDP 1000 B 1 HETATM 28 C C4 GDP . . . E 2 27.843 -21.632 27.49 1 109.9 ? C4 GDP 1000 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #