data_7OK4 # _model_server_result.job_id HzKiS5jZcX89-KaU8Xh9QQ _model_server_result.datetime_utc '2025-08-02 08:15:26' _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 7ok4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 7OK4 # _exptl.entry_id 7OK4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 613.409 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description bdaGDP _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 120 _cell.entry_id 7OK4 _cell.length_a 73.9 _cell.length_b 73.9 _cell.length_c 54.8 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OK4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 14 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 13 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C21 _struct_conn.ptnr2_label_comp_id VJB _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id VJB _struct_conn.ptnr2_auth_seq_id 201 _struct_conn.ptnr2_symmetry 1_555 _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 1.823 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C18 H29 N7 O13 P2' _chem_comp.formula_weight 613.409 _chem_comp.id VJB _chem_comp.mon_nstd_flag . _chem_comp.name bdaGDP _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[4-(propanoylamino)butyl]carbamate' # 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 O30 P29 VJB doub 348 n n O33 P27 VJB doub 349 n n O34 P27 VJB sing 350 n n O31 P29 VJB sing 351 n n P29 O28 VJB sing 352 n n P29 O32 VJB sing 353 n n P27 O28 VJB sing 354 n n P27 O26 VJB sing 355 n n N04 C05 VJB doub 356 n y N04 C03 VJB sing 357 n y O01 C02 VJB doub 358 n n C05 N06 VJB sing 359 n y C03 C02 VJB sing 360 n n C03 C36 VJB doub 361 n y O26 C25 VJB sing 362 n n C02 N40 VJB sing 363 n n O09 C08 VJB sing 364 n n C08 C07 VJB sing 365 n n C08 C10 VJB sing 366 n n N06 C36 VJB sing 367 n y N06 C07 VJB sing 368 n n C36 N37 VJB sing 369 n n N40 C38 VJB doub 370 n n C25 C24 VJB sing 371 n n C07 O35 VJB sing 372 n n C10 C24 VJB sing 373 n n C10 O11 VJB sing 374 n n N37 C38 VJB sing 375 n n C38 N39 VJB sing 376 n n C24 O35 VJB sing 377 n n O11 C12 VJB sing 378 n n O23 C12 VJB doub 379 n n C12 N13 VJB sing 380 n n N13 C14 VJB sing 381 n n C21 C20 VJB sing 382 n n C14 C15 VJB sing 383 n n C15 C16 VJB sing 384 n n C20 C19 VJB sing 385 n n C16 C17 VJB sing 386 n n N18 C19 VJB sing 387 n n N18 C17 VJB sing 388 n n C19 O22 VJB doub 389 n n C10 H1 VJB sing 390 n n C15 H2 VJB sing 391 n n C15 H3 VJB sing 392 n n C17 H4 VJB sing 393 n n C17 H5 VJB sing 394 n n C20 H6 VJB sing 395 n n C20 H7 VJB sing 396 n n C21 H8 VJB sing 397 n n C21 H9 VJB sing 398 n n C21 H10 VJB sing 399 n n C24 H11 VJB sing 400 n n C05 H12 VJB sing 401 n n C07 H13 VJB sing 402 n n C08 H14 VJB sing 403 n n C14 H15 VJB sing 404 n n C14 H16 VJB sing 405 n n C16 H17 VJB sing 406 n n C16 H18 VJB sing 407 n n C25 H19 VJB sing 408 n n C25 H20 VJB sing 409 n n N13 H21 VJB sing 410 n n N18 H22 VJB sing 411 n n N37 H23 VJB sing 412 n n N39 H24 VJB sing 413 n n N39 H25 VJB sing 414 n n O09 H26 VJB sing 415 n n O31 H27 VJB sing 416 n n O32 H28 VJB sing 417 n n O34 H29 VJB sing 418 n n # _atom_sites.entry_id 7OK4 _atom_sites.fract_transf_matrix[1][1] 0.013532 _atom_sites.fract_transf_matrix[1][2] 0.007813 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015625 _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] 0.018248 _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 VJB A 1 201 201 VJB LIG . C 3 HOH A 1 301 88 HOH HOH . C 3 HOH A 2 302 105 HOH HOH . C 3 HOH A 3 303 87 HOH HOH . C 3 HOH A 4 304 95 HOH HOH . C 3 HOH A 5 305 97 HOH HOH . C 3 HOH A 6 306 100 HOH HOH . C 3 HOH A 7 307 58 HOH HOH . C 3 HOH A 8 308 27 HOH HOH . C 3 HOH A 9 309 15 HOH HOH . C 3 HOH A 10 310 37 HOH HOH . C 3 HOH A 11 311 6 HOH HOH . C 3 HOH A 12 312 31 HOH HOH . C 3 HOH A 13 313 64 HOH HOH . C 3 HOH A 14 314 35 HOH HOH . C 3 HOH A 15 315 63 HOH HOH . C 3 HOH A 16 316 8 HOH HOH . C 3 HOH A 17 317 81 HOH HOH . C 3 HOH A 18 318 101 HOH HOH . C 3 HOH A 19 319 13 HOH HOH . C 3 HOH A 20 320 44 HOH HOH . C 3 HOH A 21 321 3 HOH HOH . C 3 HOH A 22 322 20 HOH HOH . C 3 HOH A 23 323 7 HOH HOH . C 3 HOH A 24 324 102 HOH HOH . C 3 HOH A 25 325 21 HOH HOH . C 3 HOH A 26 326 1 HOH HOH . C 3 HOH A 27 327 103 HOH HOH . C 3 HOH A 28 328 25 HOH HOH . C 3 HOH A 29 329 9 HOH HOH . C 3 HOH A 30 330 42 HOH HOH . C 3 HOH A 31 331 38 HOH HOH . C 3 HOH A 32 332 43 HOH HOH . C 3 HOH A 33 333 60 HOH HOH . C 3 HOH A 34 334 85 HOH HOH . C 3 HOH A 35 335 74 HOH HOH . C 3 HOH A 36 336 10 HOH HOH . C 3 HOH A 37 337 4 HOH HOH . C 3 HOH A 38 338 55 HOH HOH . C 3 HOH A 39 339 32 HOH HOH . C 3 HOH A 40 340 45 HOH HOH . C 3 HOH A 41 341 62 HOH HOH . C 3 HOH A 42 342 72 HOH HOH . C 3 HOH A 43 343 28 HOH HOH . C 3 HOH A 44 344 2 HOH HOH . C 3 HOH A 45 345 18 HOH HOH . C 3 HOH A 46 346 54 HOH HOH . C 3 HOH A 47 347 34 HOH HOH . C 3 HOH A 48 348 5 HOH HOH . C 3 HOH A 49 349 89 HOH HOH . C 3 HOH A 50 350 61 HOH HOH . C 3 HOH A 51 351 53 HOH HOH . C 3 HOH A 52 352 14 HOH HOH . C 3 HOH A 53 353 26 HOH HOH . C 3 HOH A 54 354 93 HOH HOH . C 3 HOH A 55 355 17 HOH HOH . C 3 HOH A 56 356 52 HOH HOH . C 3 HOH A 57 357 90 HOH HOH . C 3 HOH A 58 358 94 HOH HOH . C 3 HOH A 59 359 16 HOH HOH . C 3 HOH A 60 360 66 HOH HOH . C 3 HOH A 61 361 76 HOH HOH . C 3 HOH A 62 362 19 HOH HOH . C 3 HOH A 63 363 24 HOH HOH . C 3 HOH A 64 364 71 HOH HOH . C 3 HOH A 65 365 22 HOH HOH . C 3 HOH A 66 366 33 HOH HOH . C 3 HOH A 67 367 11 HOH HOH . C 3 HOH A 68 368 65 HOH HOH . C 3 HOH A 69 369 84 HOH HOH . C 3 HOH A 70 370 36 HOH HOH . C 3 HOH A 71 371 67 HOH HOH . C 3 HOH A 72 372 40 HOH HOH . C 3 HOH A 73 373 39 HOH HOH . C 3 HOH A 74 374 57 HOH HOH . C 3 HOH A 75 375 23 HOH HOH . C 3 HOH A 76 376 98 HOH HOH . C 3 HOH A 77 377 75 HOH HOH . C 3 HOH A 78 378 68 HOH HOH . C 3 HOH A 79 379 49 HOH HOH . C 3 HOH A 80 380 12 HOH HOH . C 3 HOH A 81 381 59 HOH HOH . C 3 HOH A 82 382 91 HOH HOH . C 3 HOH A 83 383 47 HOH HOH . C 3 HOH A 84 384 78 HOH HOH . C 3 HOH A 85 385 56 HOH HOH . C 3 HOH A 86 386 73 HOH HOH . C 3 HOH A 87 387 41 HOH HOH . C 3 HOH A 88 388 104 HOH HOH . C 3 HOH A 89 389 79 HOH HOH . C 3 HOH A 90 390 48 HOH HOH . C 3 HOH A 91 391 96 HOH HOH . C 3 HOH A 92 392 69 HOH HOH . C 3 HOH A 93 393 99 HOH HOH . C 3 HOH A 94 394 92 HOH HOH . C 3 HOH A 95 395 86 HOH HOH . C 3 HOH A 96 396 82 HOH HOH . C 3 HOH A 97 397 46 HOH HOH . C 3 HOH A 98 398 51 HOH HOH . C 3 HOH A 99 399 106 HOH HOH . C 3 HOH A 100 400 83 HOH HOH . C 3 HOH A 101 401 77 HOH HOH . C 3 HOH A 102 402 29 HOH HOH . C 3 HOH A 103 403 70 HOH HOH . C 3 HOH A 104 404 50 HOH HOH . C 3 HOH A 105 405 80 HOH HOH . C 3 HOH A 106 406 30 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 C C10 VJB . . . B 2 39.061 -5.383 19.259 1 24.44 ? C10 VJB 201 A 1 HETATM 2 C C15 VJB . . . B 2 41.355 -3.631 23.848 1 41.43 ? C15 VJB 201 A 1 HETATM 3 C C17 VJB . . . B 2 39.633 -4.623 25.414 1 60.07 ? C17 VJB 201 A 1 HETATM 4 C C20 VJB . . . B 2 37.097 -1.953 24.143 1 36.44 ? C20 VJB 201 A 1 HETATM 5 C C21 VJB . . . B 2 37.099 -2.35 22.667 1 37.67 ? C21 VJB 201 A 1 HETATM 6 C C24 VJB . . . B 2 38.016 -5.092 19.925 1 25.57 ? C24 VJB 201 A 1 HETATM 7 C C02 VJB . . . B 2 35.272 -11.45 17.959 1 24.96 ? C02 VJB 201 A 1 HETATM 8 C C03 VJB . . . B 2 35.765 -10.009 17.906 1 23.92 ? C03 VJB 201 A 1 HETATM 9 C C05 VJB . . . B 2 36.176 -7.933 17.526 1 25.22 ? C05 VJB 201 A 1 HETATM 10 C C07 VJB . . . B 2 37.956 -7.474 19.243 1 24.13 ? C07 VJB 201 A 1 HETATM 11 C C08 VJB . . . B 2 38.717 -6.789 18.419 1 24.59 ? C08 VJB 201 A 1 HETATM 12 C C12 VJB . . . B 2 40.716 -4.694 20.877 1 31.89 ? C12 VJB 201 A 1 HETATM 13 C C14 VJB . . . B 2 42.281 -3.945 22.676 1 31.78 ? C14 VJB 201 A 1 HETATM 14 C C16 VJB . . . B 2 40.81 -4.906 24.486 1 51.56 ? C16 VJB 201 A 1 HETATM 15 C C19 VJB . . . B 2 38.216 -2.631 24.936 1 51.84 ? C19 VJB 201 A 1 HETATM 16 C C25 VJB . . . B 2 37.121 -4.042 19.227 1 28.57 ? C25 VJB 201 A 1 HETATM 17 C C36 VJB . . . B 2 36.74 -9.584 18.785 1 25.08 ? C36 VJB 201 A 1 HETATM 18 C C38 VJB . . . B 2 36.856 -11.875 19.839 1 27.43 ? C38 VJB 201 A 1 HETATM 19 N N04 VJB . . . B 2 35.435 -8.962 17.139 1 25.34 ? N04 VJB 201 A 1 HETATM 20 N N06 VJB . . . B 2 36.974 -8.307 18.514 1 24.2 ? N06 VJB 201 A 1 HETATM 21 N N13 VJB . . . B 2 41.712 -5.011 21.875 1 30.62 ? N13 VJB 201 A 1 HETATM 22 N N18 VJB . . . B 2 38.563 -4.009 24.651 1 57.37 ? N18 VJB 201 A 1 HETATM 23 N N37 VJB . . . B 2 37.323 -10.492 19.782 1 24.8 ? N37 VJB 201 A 1 HETATM 24 N N39 VJB . . . B 2 37.428 -12.77 20.813 1 31.88 ? N39 VJB 201 A 1 HETATM 25 N N40 VJB . . . B 2 35.833 -12.331 18.929 1 25.91 ? N40 VJB 201 A 1 HETATM 26 O O01 VJB . . . B 2 34.423 -11.836 17.213 1 24.75 ? O01 VJB 201 A 1 HETATM 27 O O09 VJB . . . B 2 39.938 -7.492 18.118 1 26.88 ? O09 VJB 201 A 1 HETATM 28 O O11 VJB . . . B 2 40.163 -5.742 20.136 1 26.13 ? O11 VJB 201 A 1 HETATM 29 O O22 VJB . . . B 2 38.815 -2.041 25.777 1 51.66 ? O22 VJB 201 A 1 HETATM 30 O O23 VJB . . . B 2 40.374 -3.568 20.699 1 30.32 ? O23 VJB 201 A 1 HETATM 31 O O26 VJB . . . B 2 36.847 -4.494 17.932 1 24.94 ? O26 VJB 201 A 1 HETATM 32 O O28 VJB . . . B 2 35.267 -2.553 17.469 1 23.36 ? O28 VJB 201 A 1 HETATM 33 O O30 VJB . . . B 2 34.877 -1.125 15.382 1 26.53 -1 O30 VJB 201 A 1 HETATM 34 O O31 VJB . . . B 2 32.934 -1.802 16.784 1 25.8 -1 O31 VJB 201 A 1 HETATM 35 O O32 VJB . . . B 2 34.551 -0.12 17.646 1 26.49 ? O32 VJB 201 A 1 HETATM 36 O O33 VJB . . . B 2 36.267 -3.957 15.5 1 24.8 -1 O33 VJB 201 A 1 HETATM 37 O O34 VJB . . . B 2 37.762 -2.394 16.78 1 27.21 ? O34 VJB 201 A 1 HETATM 38 O O35 VJB . . . B 2 37.153 -6.436 20.028 1 25.5 ? O35 VJB 201 A 1 HETATM 39 P P27 VJB . . . B 2 36.577 -3.324 16.83 1 24.65 ? P27 VJB 201 A 1 HETATM 40 P P29 VJB . . . B 2 34.372 -1.36 16.791 1 24.98 ? P29 VJB 201 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #