data_3CBQ # _model_server_result.job_id yvnZKxQNmWD4rNrY1zqw7g _model_server_result.datetime_utc '2024-11-04 22:51:28' _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 3cbq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 3CBQ # _exptl.entry_id 3CBQ _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 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 3CBQ _cell.length_a 64.143 _cell.length_b 64.33 _cell.length_c 73.204 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CBQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OG SER 37 A SER 128 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc2 B MG MG . A MG 301 1_555 C O1B GDP . A GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc3 B MG MG . A MG 301 1_555 G O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc4 B MG MG . A MG 301 1_555 G O HOH . A HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc5 B MG MG . A MG 301 1_555 G O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc6 B MG MG . A MG 301 1_555 G O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? # _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 92 n n PB O2B GDP sing 93 n n PB O3B GDP sing 94 n n PB O3A GDP sing 95 n n O2B HOB2 GDP sing 96 n n O3B HOB3 GDP sing 97 n n O3A PA GDP sing 98 n n PA O1A GDP doub 99 n n PA O2A GDP sing 100 n n PA O5' GDP sing 101 n n O2A HOA2 GDP sing 102 n n O5' C5' GDP sing 103 n n C5' C4' GDP sing 104 n n C5' H5' GDP sing 105 n n C5' "H5''" GDP sing 106 n n C4' O4' GDP sing 107 n n C4' C3' GDP sing 108 n n C4' H4' GDP sing 109 n n O4' C1' GDP sing 110 n n C3' O3' GDP sing 111 n n C3' C2' GDP sing 112 n n C3' H3' GDP sing 113 n n O3' HO3' GDP sing 114 n n C2' O2' GDP sing 115 n n C2' C1' GDP sing 116 n n C2' H2' GDP sing 117 n n O2' HO2' GDP sing 118 n n C1' N9 GDP sing 119 n n C1' H1' GDP sing 120 n n N9 C8 GDP sing 121 n y N9 C4 GDP sing 122 n y C8 N7 GDP doub 123 n y C8 H8 GDP sing 124 n n N7 C5 GDP sing 125 n y C5 C6 GDP sing 126 n n C5 C4 GDP doub 127 n y C6 O6 GDP doub 128 n n C6 N1 GDP sing 129 n n N1 C2 GDP sing 130 n n N1 HN1 GDP sing 131 n n C2 N2 GDP sing 132 n n C2 N3 GDP doub 133 n n N2 HN21 GDP sing 134 n n N2 HN22 GDP sing 135 n n N3 C4 GDP sing 136 n n # _atom_sites.entry_id 3CBQ _atom_sites.fract_transf_matrix[1][1] 0.01559 _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] 0.015545 _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] 0.01366 _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 MG A 1 301 301 MG MG . C 3 GDP A 1 302 302 GDP GDP . D 4 EDO A 1 303 303 EDO EDO . E 4 EDO A 1 304 304 EDO EDO . F 5 UNX A 1 1 1 UNX UNX . G 6 HOH A 1 305 1 HOH HOH . G 6 HOH A 2 306 2 HOH HOH . G 6 HOH A 3 307 3 HOH HOH . G 6 HOH A 4 308 4 HOH HOH . G 6 HOH A 5 309 5 HOH HOH . G 6 HOH A 6 310 6 HOH HOH . G 6 HOH A 7 311 7 HOH HOH . G 6 HOH A 8 312 8 HOH HOH . G 6 HOH A 9 313 9 HOH HOH . G 6 HOH A 10 314 10 HOH HOH . G 6 HOH A 11 315 11 HOH HOH . G 6 HOH A 12 316 12 HOH HOH . G 6 HOH A 13 317 13 HOH HOH . G 6 HOH A 14 318 14 HOH HOH . G 6 HOH A 15 319 15 HOH HOH . G 6 HOH A 16 320 16 HOH HOH . G 6 HOH A 17 321 17 HOH HOH . G 6 HOH A 18 322 18 HOH HOH . G 6 HOH A 19 323 19 HOH HOH . G 6 HOH A 20 324 20 HOH HOH . G 6 HOH A 21 325 21 HOH HOH . G 6 HOH A 22 326 22 HOH HOH . G 6 HOH A 23 327 23 HOH HOH . G 6 HOH A 24 328 24 HOH HOH . G 6 HOH A 25 329 25 HOH HOH . G 6 HOH A 26 330 26 HOH HOH . G 6 HOH A 27 331 27 HOH HOH . G 6 HOH A 28 332 28 HOH HOH . G 6 HOH A 29 333 29 HOH HOH . G 6 HOH A 30 334 30 HOH HOH . G 6 HOH A 31 335 31 HOH HOH . G 6 HOH A 32 336 32 HOH HOH . G 6 HOH A 33 337 33 HOH HOH . G 6 HOH A 34 338 34 HOH HOH . G 6 HOH A 35 339 35 HOH HOH . G 6 HOH A 36 340 36 HOH HOH . G 6 HOH A 37 341 37 HOH HOH . G 6 HOH A 38 342 38 HOH HOH . G 6 HOH A 39 343 39 HOH HOH . G 6 HOH A 40 344 40 HOH HOH . G 6 HOH A 41 345 41 HOH HOH . G 6 HOH A 42 346 42 HOH HOH . G 6 HOH A 43 347 43 HOH HOH . G 6 HOH A 44 348 44 HOH HOH . G 6 HOH A 45 349 45 HOH HOH . G 6 HOH A 46 350 46 HOH HOH . G 6 HOH A 47 351 47 HOH HOH . G 6 HOH A 48 352 48 HOH HOH . G 6 HOH A 49 353 49 HOH HOH . G 6 HOH A 50 354 50 HOH HOH . G 6 HOH A 51 355 51 HOH HOH . G 6 HOH A 52 356 52 HOH HOH . G 6 HOH A 53 357 53 HOH HOH . G 6 HOH A 54 358 54 HOH HOH . G 6 HOH A 55 359 55 HOH HOH . G 6 HOH A 56 360 56 HOH HOH . G 6 HOH A 57 361 57 HOH HOH . G 6 HOH A 58 362 58 HOH HOH . G 6 HOH A 59 363 59 HOH HOH . G 6 HOH A 60 364 60 HOH HOH . G 6 HOH A 61 365 61 HOH HOH . G 6 HOH A 62 366 62 HOH HOH . G 6 HOH A 63 367 63 HOH HOH . G 6 HOH A 64 368 64 HOH HOH . G 6 HOH A 65 369 65 HOH HOH . G 6 HOH A 66 370 66 HOH HOH . G 6 HOH A 67 371 67 HOH HOH . G 6 HOH A 68 372 68 HOH HOH . G 6 HOH A 69 373 69 HOH HOH . G 6 HOH A 70 374 70 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 . . . C 3 11.071 26.118 0.785 1 17.56 ? PB GDP 302 A 1 HETATM 2 O O1B GDP . . . C 3 10.579 26.066 2.215 1 16.4 ? O1B GDP 302 A 1 HETATM 3 O O2B GDP . . . C 3 12.285 26.996 0.782 1 18.83 ? O2B GDP 302 A 1 HETATM 4 O O3B GDP . . . C 3 11.351 24.801 0.103 1 15.81 ? O3B GDP 302 A 1 HETATM 5 O O3A GDP . . . C 3 9.946 26.855 -0.134 1 19.64 ? O3A GDP 302 A 1 HETATM 6 P PA GDP . . . C 3 8.653 27.677 0.346 1 19.71 ? PA GDP 302 A 1 HETATM 7 O O1A GDP . . . C 3 9.02 28.778 1.301 1 18.47 ? O1A GDP 302 A 1 HETATM 8 O O2A GDP . . . C 3 7.584 26.732 0.88 1 21.25 ? O2A GDP 302 A 1 HETATM 9 O O5' GDP . . . C 3 8.162 28.159 -1.063 1 19.14 ? O5' GDP 302 A 1 HETATM 10 C C5' GDP . . . C 3 8.902 29.155 -1.765 1 21.06 ? C5' GDP 302 A 1 HETATM 11 C C4' GDP . . . C 3 7.931 30.047 -2.506 1 23.12 ? C4' GDP 302 A 1 HETATM 12 O O4' GDP . . . C 3 7.253 29.219 -3.448 1 21.53 ? O4' GDP 302 A 1 HETATM 13 C C3' GDP . . . C 3 6.88 30.681 -1.605 1 22.84 ? C3' GDP 302 A 1 HETATM 14 O O3' GDP . . . C 3 6.575 32.011 -2.073 1 21.25 ? O3' GDP 302 A 1 HETATM 15 C C2' GDP . . . C 3 5.668 29.808 -1.785 1 23.39 ? C2' GDP 302 A 1 HETATM 16 O O2' GDP . . . C 3 4.43 30.492 -1.601 1 25.91 ? O2' GDP 302 A 1 HETATM 17 C C1' GDP . . . C 3 5.842 29.363 -3.213 1 22.53 ? C1' GDP 302 A 1 HETATM 18 N N9 GDP . . . C 3 5.245 28.06 -3.457 1 22.3 ? N9 GDP 302 A 1 HETATM 19 C C8 GDP . . . C 3 5.477 26.954 -2.724 1 20.56 ? C8 GDP 302 A 1 HETATM 20 N N7 GDP . . . C 3 4.811 25.914 -3.245 1 16.89 ? N7 GDP 302 A 1 HETATM 21 C C5 GDP . . . C 3 4.146 26.358 -4.333 1 22.26 ? C5 GDP 302 A 1 HETATM 22 C C6 GDP . . . C 3 3.245 25.779 -5.337 1 19.89 ? C6 GDP 302 A 1 HETATM 23 O O6 GDP . . . C 3 2.904 24.588 -5.314 1 19.06 ? O6 GDP 302 A 1 HETATM 24 N N1 GDP . . . C 3 2.773 26.575 -6.296 1 21.61 ? N1 GDP 302 A 1 HETATM 25 C C2 GDP . . . C 3 3.101 27.879 -6.387 1 21.99 ? C2 GDP 302 A 1 HETATM 26 N N2 GDP . . . C 3 2.597 28.622 -7.391 1 22.05 ? N2 GDP 302 A 1 HETATM 27 N N3 GDP . . . C 3 3.922 28.475 -5.504 1 23.13 ? N3 GDP 302 A 1 HETATM 28 C C4 GDP . . . C 3 4.452 27.778 -4.479 1 19.38 ? C4 GDP 302 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #