data_3V7W # _model_server_result.job_id FdD37Ap8E-FGQBqfulISww _model_server_result.datetime_utc '2024-11-08 22:26:15' _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 3v7w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 3V7W # _exptl.entry_id 3V7W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.254 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-azido-5'-deoxyadenosine" _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 3V7W _cell.length_a 62.912 _cell.length_b 74.026 _cell.length_c 118.419 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V7W _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 62.912 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 62.912 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N # _chem_comp.formula 'C10 H12 N8 O3' _chem_comp.formula_weight 292.254 _chem_comp.id ZAS _chem_comp.mon_nstd_flag . _chem_comp.name "5'-azido-5'-deoxyadenosine" _chem_comp.type non-polymer _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 N53 N52 ZAS doub 409 n n N6 C6 ZAS sing 410 n n N52 N51 ZAS doub 411 n n C6 N1 ZAS doub 412 n y C6 C5 ZAS sing 413 n y N1 C2 ZAS sing 414 n y N51 C5' ZAS sing 415 n n N7 C5 ZAS sing 416 n y N7 C8 ZAS doub 417 n y C5 C4 ZAS doub 418 n y C8 N9 ZAS sing 419 n y C2 N3 ZAS doub 420 n y C4 N3 ZAS sing 421 n y C4 N9 ZAS sing 422 n y O4' C4' ZAS sing 423 n n O4' C1' ZAS sing 424 n n N9 C1' ZAS sing 425 n n C5' C4' ZAS sing 426 n n C4' C3' ZAS sing 427 n n C1' C2' ZAS sing 428 n n C2' C3' ZAS sing 429 n n C2' O2' ZAS sing 430 n n C3' O3' ZAS sing 431 n n C5' H5' ZAS sing 432 n n C5' "H5''" ZAS sing 433 n n C4' H4' ZAS sing 434 n n C3' H3' ZAS sing 435 n n O3' HO3' ZAS sing 436 n n C2' H2' ZAS sing 437 n n O2' HO8' ZAS sing 438 n n C1' H1' ZAS sing 439 n n C8 H8 ZAS sing 440 n n C2 H2 ZAS sing 441 n n N6 H61 ZAS sing 442 n n N6 H62 ZAS sing 443 n n # _atom_sites.entry_id 3V7W _atom_sites.fract_transf_matrix[1][1] 0.015895 _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] 0.013509 _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] 0.008445 _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 ZAS A 1 301 1 ZAS ZAS . C 2 ZAS A 1 302 2 ZAS ZAS . D 3 CIT A 1 303 1 CIT CIT . E 4 GOL A 1 304 3 GOL GOL . F 5 HOH A 1 401 1 HOH HOH . F 5 HOH A 2 402 2 HOH HOH . F 5 HOH A 3 403 3 HOH HOH . F 5 HOH A 4 404 5 HOH HOH . F 5 HOH A 5 405 6 HOH HOH . F 5 HOH A 6 406 7 HOH HOH . F 5 HOH A 7 407 9 HOH HOH . F 5 HOH A 8 408 12 HOH HOH . F 5 HOH A 9 409 16 HOH HOH . F 5 HOH A 10 410 17 HOH HOH . F 5 HOH A 11 411 19 HOH HOH . F 5 HOH A 12 412 20 HOH HOH . F 5 HOH A 13 413 21 HOH HOH . F 5 HOH A 14 414 23 HOH HOH . F 5 HOH A 15 415 24 HOH HOH . F 5 HOH A 16 416 26 HOH HOH . F 5 HOH A 17 417 27 HOH HOH . F 5 HOH A 18 418 28 HOH HOH . F 5 HOH A 19 419 29 HOH HOH . F 5 HOH A 20 420 30 HOH HOH . F 5 HOH A 21 421 32 HOH HOH . F 5 HOH A 22 422 34 HOH HOH . F 5 HOH A 23 423 36 HOH HOH . F 5 HOH A 24 424 38 HOH HOH . F 5 HOH A 25 425 39 HOH HOH . F 5 HOH A 26 426 45 HOH HOH . F 5 HOH A 27 427 46 HOH HOH . F 5 HOH A 28 428 48 HOH HOH . F 5 HOH A 29 429 52 HOH HOH . F 5 HOH A 30 430 63 HOH HOH . F 5 HOH A 31 431 65 HOH HOH . F 5 HOH A 32 432 67 HOH HOH . F 5 HOH A 33 433 68 HOH HOH . F 5 HOH A 34 434 69 HOH HOH . F 5 HOH A 35 435 72 HOH HOH . F 5 HOH A 36 436 74 HOH HOH . F 5 HOH A 37 437 75 HOH HOH . F 5 HOH A 38 438 77 HOH HOH . F 5 HOH A 39 439 79 HOH HOH . F 5 HOH A 40 440 82 HOH HOH . F 5 HOH A 41 441 84 HOH HOH . F 5 HOH A 42 442 86 HOH HOH . F 5 HOH A 43 443 89 HOH HOH . F 5 HOH A 44 444 94 HOH HOH . F 5 HOH A 45 445 105 HOH HOH . F 5 HOH A 46 446 108 HOH HOH . F 5 HOH A 47 447 110 HOH HOH . F 5 HOH A 48 448 114 HOH HOH . F 5 HOH A 49 449 118 HOH HOH . F 5 HOH A 50 450 119 HOH HOH . F 5 HOH A 51 451 126 HOH HOH . F 5 HOH A 52 452 128 HOH HOH . F 5 HOH A 53 453 130 HOH HOH . F 5 HOH A 54 454 141 HOH HOH . F 5 HOH A 55 455 145 HOH HOH . F 5 HOH A 56 456 146 HOH HOH . F 5 HOH A 57 457 148 HOH HOH . F 5 HOH A 58 458 149 HOH HOH . F 5 HOH A 59 459 150 HOH HOH . F 5 HOH A 60 460 152 HOH HOH . F 5 HOH A 61 461 153 HOH HOH . F 5 HOH A 62 462 154 HOH HOH . F 5 HOH A 63 463 159 HOH HOH . F 5 HOH A 64 464 168 HOH HOH . F 5 HOH A 65 465 207 HOH HOH . F 5 HOH A 66 466 209 HOH HOH . F 5 HOH A 67 467 211 HOH HOH . F 5 HOH A 68 468 212 HOH HOH . F 5 HOH A 69 469 215 HOH HOH . F 5 HOH A 70 470 216 HOH HOH . F 5 HOH A 71 471 217 HOH HOH . F 5 HOH A 72 472 218 HOH HOH . F 5 HOH A 73 473 219 HOH HOH . F 5 HOH A 74 474 225 HOH HOH . F 5 HOH A 75 475 227 HOH HOH . F 5 HOH A 76 476 233 HOH HOH . F 5 HOH A 77 477 234 HOH HOH . F 5 HOH A 78 478 235 HOH HOH . F 5 HOH A 79 479 236 HOH HOH . F 5 HOH A 80 480 238 HOH HOH . F 5 HOH A 81 481 239 HOH HOH . F 5 HOH A 82 482 241 HOH HOH . F 5 HOH A 83 483 242 HOH HOH . F 5 HOH A 84 484 244 HOH HOH . F 5 HOH A 85 485 245 HOH HOH . F 5 HOH A 86 486 246 HOH HOH . F 5 HOH A 87 487 247 HOH HOH . F 5 HOH A 88 488 249 HOH HOH . F 5 HOH A 89 489 250 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 N N53 ZAS . . . C 2 15.261 10.252 13.635 0.79 47.02 ? N53 ZAS 302 A 1 HETATM 2 N N52 ZAS . . . C 2 14.543 9.848 12.683 0.83 50.55 ? N52 ZAS 302 A 1 HETATM 3 N N51 ZAS . . . C 2 13.813 9.455 11.7 0.88 49.63 ? N51 ZAS 302 A 1 HETATM 4 C C5' ZAS . . . C 2 13.957 10.067 10.384 1 39.96 ? C5' ZAS 302 A 1 HETATM 5 C C4' ZAS . . . C 2 15.31 9.719 9.833 1 36.73 ? C4' ZAS 302 A 1 HETATM 6 O O4' ZAS . . . C 2 15.428 8.353 9.643 1 37.93 ? O4' ZAS 302 A 1 HETATM 7 C C3' ZAS . . . C 2 15.455 10.227 8.428 1 32.36 ? C3' ZAS 302 A 1 HETATM 8 O O3' ZAS . . . C 2 15.742 11.593 8.44 1 29.35 ? O3' ZAS 302 A 1 HETATM 9 C C2' ZAS . . . C 2 16.62 9.385 7.932 1 34.81 ? C2' ZAS 302 A 1 HETATM 10 O O2' ZAS . . . C 2 17.792 10.079 8.056 1 30.17 ? O2' ZAS 302 A 1 HETATM 11 C C1' ZAS . . . C 2 16.635 8.2 8.885 1 36.68 ? C1' ZAS 302 A 1 HETATM 12 N N9 ZAS . . . C 2 16.766 6.886 8.263 1 36.7 ? N9 ZAS 302 A 1 HETATM 13 C C8 ZAS . . . C 2 15.841 6.188 7.659 1 36.87 ? C8 ZAS 302 A 1 HETATM 14 N N7 ZAS . . . C 2 16.339 5.053 7.246 1 36.04 ? N7 ZAS 302 A 1 HETATM 15 C C5 ZAS . . . C 2 17.595 5.002 7.583 1 39.52 ? C5 ZAS 302 A 1 HETATM 16 C C4 ZAS . . . C 2 17.856 6.172 8.237 1 38.97 ? C4 ZAS 302 A 1 HETATM 17 N N3 ZAS . . . C 2 19.067 6.389 8.684 1 37.53 ? N3 ZAS 302 A 1 HETATM 18 C C2 ZAS . . . C 2 19.994 5.502 8.53 1 35.51 ? C2 ZAS 302 A 1 HETATM 19 N N1 ZAS . . . C 2 19.788 4.381 7.918 1 36.18 ? N1 ZAS 302 A 1 HETATM 20 C C6 ZAS . . . C 2 18.617 4.079 7.421 1 40.19 ? C6 ZAS 302 A 1 HETATM 21 N N6 ZAS . . . C 2 18.467 2.934 6.831 1 27.48 ? N6 ZAS 302 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #