data_7EYX # _model_server_result.job_id 9SkKiY19QlOB490OgspSDQ _model_server_result.datetime_utc '2024-10-20 00:29:41' _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 7eyx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 7EYX # _exptl.entry_id 7EYX _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 1 _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 7EYX _cell.length_a 36.01 _cell.length_b 37.34 _cell.length_c 100.35 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EYX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 7EYX _atom_sites.fract_transf_matrix[1][1] 0.02777 _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] 0.026781 _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] 0.009965 _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 B 2 GDP A 1 201 201 GDP GDP . C 3 HOH A 1 301 60 HOH HOH . C 3 HOH A 2 302 10 HOH HOH . C 3 HOH A 3 303 11 HOH HOH . C 3 HOH A 4 304 62 HOH HOH . C 3 HOH A 5 305 89 HOH HOH . C 3 HOH A 6 306 97 HOH HOH . C 3 HOH A 7 307 33 HOH HOH . C 3 HOH A 8 308 80 HOH HOH . C 3 HOH A 9 309 40 HOH HOH . C 3 HOH A 10 310 32 HOH HOH . C 3 HOH A 11 311 26 HOH HOH . C 3 HOH A 12 312 70 HOH HOH . C 3 HOH A 13 313 2 HOH HOH . C 3 HOH A 14 314 45 HOH HOH . C 3 HOH A 15 315 79 HOH HOH . C 3 HOH A 16 316 31 HOH HOH . C 3 HOH A 17 317 77 HOH HOH . C 3 HOH A 18 318 35 HOH HOH . C 3 HOH A 19 319 28 HOH HOH . C 3 HOH A 20 320 92 HOH HOH . C 3 HOH A 21 321 8 HOH HOH . C 3 HOH A 22 322 4 HOH HOH . C 3 HOH A 23 323 78 HOH HOH . C 3 HOH A 24 324 17 HOH HOH . C 3 HOH A 25 325 85 HOH HOH . C 3 HOH A 26 326 44 HOH HOH . C 3 HOH A 27 327 75 HOH HOH . C 3 HOH A 28 328 69 HOH HOH . C 3 HOH A 29 329 6 HOH HOH . C 3 HOH A 30 330 76 HOH HOH . C 3 HOH A 31 331 25 HOH HOH . C 3 HOH A 32 332 88 HOH HOH . C 3 HOH A 33 333 59 HOH HOH . C 3 HOH A 34 334 87 HOH HOH . C 3 HOH A 35 335 15 HOH HOH . C 3 HOH A 36 336 22 HOH HOH . C 3 HOH A 37 337 48 HOH HOH . C 3 HOH A 38 338 1 HOH HOH . C 3 HOH A 39 339 14 HOH HOH . C 3 HOH A 40 340 27 HOH HOH . C 3 HOH A 41 341 72 HOH HOH . C 3 HOH A 42 342 36 HOH HOH . C 3 HOH A 43 343 24 HOH HOH . C 3 HOH A 44 344 67 HOH HOH . C 3 HOH A 45 345 7 HOH HOH . C 3 HOH A 46 346 18 HOH HOH . C 3 HOH A 47 347 81 HOH HOH . C 3 HOH A 48 348 95 HOH HOH . C 3 HOH A 49 349 73 HOH HOH . C 3 HOH A 50 350 84 HOH HOH . C 3 HOH A 51 351 94 HOH HOH . C 3 HOH A 52 352 20 HOH HOH . C 3 HOH A 53 353 74 HOH HOH . C 3 HOH A 54 354 96 HOH HOH . C 3 HOH A 55 355 98 HOH HOH . C 3 HOH A 56 356 66 HOH HOH . C 3 HOH A 57 357 30 HOH HOH . C 3 HOH A 58 358 83 HOH HOH . C 3 HOH A 59 359 29 HOH HOH . # 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 . . . B 2 9.849 6.837 -17.504 1 11.31 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 10.05 5.747 -18.523 1 9.66 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 8.848 7.889 -17.912 1 9.01 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 9.504 6.379 -16.114 1 10.67 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 11.256 7.616 -17.361 1 8.72 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 12.479 7.632 -18.404 1 9.77 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 11.984 8.157 -19.733 1 12.47 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 13.202 6.317 -18.374 1 7.6 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 13.476 8.69 -17.674 1 8.26 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 13.085 10.032 -17.471 1 8.82 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 14.31 10.919 -17.461 1 9.23 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 15.135 10.6 -16.304 1 9.07 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 15.32 10.852 -18.638 1 9.35 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 15.856 12.149 -18.846 1 10.08 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 16.349 9.816 -18.2 1 10.01 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 17.67 10 -18.687 1 10.67 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 16.43 10.074 -16.691 1 8.95 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 16.784 8.987 -15.795 1 8.54 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 16.172 7.799 -15.714 1 8 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 16.763 7.054 -14.74 1 7.88 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 17.779 7.799 -14.226 1 8.38 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 18.789 7.623 -13.166 1 8.71 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 18.84 6.558 -12.512 1 11.54 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 19.639 8.629 -12.901 1 9.39 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 19.583 9.772 -13.619 1 11.58 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 20.434 10.754 -13.342 1 16.57 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 18.676 10.026 -14.595 1 9.45 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 17.761 9.07 -14.908 1 8.8 ? C4 GDP 201 A 1 HETATM 29 H H4' GDP . . . B 2 13.838 11.911 -17.491 1 10.97 ? H4' GDP 201 A 1 HETATM 30 H H3' GDP . . . B 2 14.889 10.557 -19.605 1 11.2 ? H3' GDP 201 A 1 HETATM 31 H HO3' GDP . . . B 2 16.794 12.078 -19.069 1 11.99 ? HO3' GDP 201 A 1 HETATM 32 H H2' GDP . . . B 2 16.043 8.824 -18.562 1 12.03 ? H2' GDP 201 A 1 HETATM 33 H HO2' GDP . . . B 2 17.649 10.094 -19.649 1 12.82 ? HO2' GDP 201 A 1 HETATM 34 H H1' GDP . . . B 2 17.288 10.752 -16.586 1 10.63 ? H1' GDP 201 A 1 HETATM 35 H H8 GDP . . . B 2 15.337 7.481 -16.326 1 9.49 ? H8 GDP 201 A 1 HETATM 36 H HN1 GDP . . . B 2 20.343 8.528 -12.142 1 11.16 ? HN1 GDP 201 A 1 HETATM 37 H HN21 GDP . . . B 2 20.376 11.619 -13.85 1 19.91 ? HN21 GDP 201 A 1 HETATM 38 H HN22 GDP . . . B 2 21.113 10.636 -12.628 1 19.91 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #