data_5V68 # _model_server_result.job_id jMSXCF4KN5Nux1E-qjsBkg _model_server_result.datetime_utc '2024-11-15 06:25:36' _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 5v68 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 5V68 # _exptl.entry_id 5V68 _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 90 _cell.angle_gamma 90 _cell.entry_id 5V68 _cell.length_a 73.11 _cell.length_b 180.85 _cell.length_c 220.16 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V68 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,B,C,G,H 1 1 D,E,F,I,J 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 G N N ? 2 I 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 5V68 _atom_sites.fract_transf_matrix[1][1] 0.013678 _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] 0.005529 _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] 0.004542 _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 G 2 GDP B 1 401 401 GDP GDP . H 3 PO4 C 1 401 402 PO4 PO4 . I 2 GDP E 1 401 401 GDP GDP . J 3 PO4 F 1 401 402 PO4 PO4 . # 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 . . . I 2 -2.665 40.241 51.459 1 115.37 ? PB GDP 401 E 1 HETATM 2 O O1B GDP . . . I 2 -1.784 40.609 50.29 1 121.63 ? O1B GDP 401 E 1 HETATM 3 O O2B GDP . . . I 2 -1.83 39.693 52.584 1 108.6 ? O2B GDP 401 E 1 HETATM 4 O O3B GDP . . . I 2 -3.876 39.382 51.172 1 103.83 ? O3B GDP 401 E 1 HETATM 5 O O3A GDP . . . I 2 -3.278 41.664 51.956 1 130.35 ? O3A GDP 401 E 1 HETATM 6 P PA GDP . . . I 2 -4.153 42.696 51.047 1 137.07 ? PA GDP 401 E 1 HETATM 7 O O1A GDP . . . I 2 -3.956 42.334 49.587 1 142.18 ? O1A GDP 401 E 1 HETATM 8 O O2A GDP . . . I 2 -5.564 42.787 51.591 1 124.31 ? O2A GDP 401 E 1 HETATM 9 O O5' GDP . . . I 2 -3.492 44.145 51.324 1 128.42 ? O5' GDP 401 E 1 HETATM 10 C C5' GDP . . . I 2 -2.353 44.603 50.599 1 133.29 ? C5' GDP 401 E 1 HETATM 11 C C4' GDP . . . I 2 -2.287 46.123 50.507 1 138.76 ? C4' GDP 401 E 1 HETATM 12 O O4' GDP . . . I 2 -3.314 46.547 49.61 1 146.77 ? O4' GDP 401 E 1 HETATM 13 C C3' GDP . . . I 2 -2.476 46.86 51.831 1 145.36 ? C3' GDP 401 E 1 HETATM 14 O O3' GDP . . . I 2 -1.282 47.552 52.214 1 133.75 ? O3' GDP 401 E 1 HETATM 15 C C2' GDP . . . I 2 -3.624 47.835 51.612 1 151.16 ? C2' GDP 401 E 1 HETATM 16 O O2' GDP . . . I 2 -3.188 49.197 51.77 1 151.28 ? O2' GDP 401 E 1 HETATM 17 C C1' GDP . . . I 2 -4.142 47.563 50.189 1 151.29 ? C1' GDP 401 E 1 HETATM 18 N N9 GDP . . . I 2 -5.579 47.146 50.065 1 148.31 ? N9 GDP 401 E 1 HETATM 19 C C8 GDP . . . I 2 -6.467 46.727 50.999 1 151.46 ? C8 GDP 401 E 1 HETATM 20 N N7 GDP . . . I 2 -7.68 46.454 50.451 1 141.01 ? N7 GDP 401 E 1 HETATM 21 C C5 GDP . . . I 2 -7.581 46.695 49.148 1 136.86 ? C5 GDP 401 E 1 HETATM 22 C C6 GDP . . . I 2 -8.478 46.609 47.99 1 142.89 ? C6 GDP 401 E 1 HETATM 23 O O6 GDP . . . I 2 -9.65 46.236 48.149 1 142.89 ? O6 GDP 401 E 1 HETATM 24 N N1 GDP . . . I 2 -7.993 46.949 46.783 1 159.86 ? N1 GDP 401 E 1 HETATM 25 C C2 GDP . . . I 2 -6.709 47.361 46.609 1 165.99 ? C2 GDP 401 E 1 HETATM 26 N N2 GDP . . . I 2 -6.253 47.691 45.371 1 166.48 ? N2 GDP 401 E 1 HETATM 27 N N3 GDP . . . I 2 -5.83 47.457 47.642 1 158.41 ? N3 GDP 401 E 1 HETATM 28 C C4 GDP . . . I 2 -6.206 47.139 48.899 1 144.98 ? C4 GDP 401 E 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #