data_5OXF # _model_server_result.job_id wkTYPZDss_ujK3VboDdY6w _model_server_result.datetime_utc '2024-11-22 18:30:04' _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 5oxf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1000}' # _entry.id 5OXF # _exptl.entry_id 5OXF _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 4 _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 5OXF _cell.length_a 114.717 _cell.length_b 228.675 _cell.length_c 318.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OXF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H 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 5OXF _atom_sites.fract_transf_matrix[1][1] 0.008717 _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] 0.004373 _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] 0.003137 _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 3 GDP A 1 1000 1000 GDP GDP . F 3 GDP B 1 1000 1000 GDP GDP . G 3 GDP C 1 1000 1000 GDP GDP . H 3 GDP D 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 . . . F 3 20.684 -62.323 -65.809 1 209.16 ? PB GDP 1000 B 1 HETATM 2 O O1B GDP . . . F 3 21.436 -62.812 -67.024 1 209.71 -1 O1B GDP 1000 B 1 HETATM 3 O O2B GDP . . . F 3 19.53 -63.237 -65.47 1 159.42 ? O2B GDP 1000 B 1 HETATM 4 O O3B GDP . . . F 3 20.167 -60.929 -66.056 1 208.58 ? O3B GDP 1000 B 1 HETATM 5 O O3A GDP . . . F 3 21.692 -62.269 -64.556 1 188.31 ? O3A GDP 1000 B 1 HETATM 6 P PA GDP . . . F 3 22.681 -63.484 -64.201 1 189.94 ? PA GDP 1000 B 1 HETATM 7 O O1A GDP . . . F 3 22.584 -64.534 -65.281 1 271 ? O1A GDP 1000 B 1 HETATM 8 O O2A GDP . . . F 3 22.283 -64.042 -62.858 1 180.77 -1 O2A GDP 1000 B 1 HETATM 9 O O5' GDP . . . F 3 24.198 -62.954 -64.109 1 197.7 ? O5' GDP 1000 B 1 HETATM 10 C C5' GDP . . . F 3 24.975 -62.756 -65.288 1 221.64 ? C5' GDP 1000 B 1 HETATM 11 C C4' GDP . . . F 3 26.434 -63.102 -65.005 1 236.12 ? C4' GDP 1000 B 1 HETATM 12 O O4' GDP . . . F 3 26.981 -62.174 -64.067 1 234.4 ? O4' GDP 1000 B 1 HETATM 13 C C3' GDP . . . F 3 26.59 -64.476 -64.378 1 253.82 ? C3' GDP 1000 B 1 HETATM 14 O O3' GDP . . . F 3 27.737 -65.108 -64.951 1 277.93 ? O3' GDP 1000 B 1 HETATM 15 C C2' GDP . . . F 3 26.84 -64.209 -62.908 1 245.38 ? C2' GDP 1000 B 1 HETATM 16 O O2' GDP . . . F 3 27.698 -65.211 -62.359 1 299.85 ? O2' GDP 1000 B 1 HETATM 17 C C1' GDP . . . F 3 27.521 -62.852 -62.93 1 248.85 ? C1' GDP 1000 B 1 HETATM 18 N N9 GDP . . . F 3 27.243 -62.043 -61.716 1 260.81 ? N9 GDP 1000 B 1 HETATM 19 C C8 GDP . . . F 3 26.035 -61.837 -61.167 1 246.41 ? C8 GDP 1000 B 1 HETATM 20 N N7 GDP . . . F 3 26.116 -61.036 -60.074 1 252.48 ? N7 GDP 1000 B 1 HETATM 21 C C5 GDP . . . F 3 27.411 -60.705 -59.913 1 272.56 ? C5 GDP 1000 B 1 HETATM 22 C C6 GDP . . . F 3 28.202 -59.886 -58.961 1 273.97 ? C6 GDP 1000 B 1 HETATM 23 O O6 GDP . . . F 3 27.658 -59.289 -58.006 1 259.34 ? O6 GDP 1000 B 1 HETATM 24 N N1 GDP . . . F 3 29.524 -59.803 -59.151 1 274.21 ? N1 GDP 1000 B 1 HETATM 25 C C2 GDP . . . F 3 30.147 -60.432 -60.166 1 280.55 ? C2 GDP 1000 B 1 HETATM 26 N N2 GDP . . . F 3 31.489 -60.296 -60.288 1 277.31 ? N2 GDP 1000 B 1 HETATM 27 N N3 GDP . . . F 3 29.487 -61.197 -61.074 1 286.39 ? N3 GDP 1000 B 1 HETATM 28 C C4 GDP . . . F 3 28.146 -61.368 -61.001 1 277.74 ? C4 GDP 1000 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #