data_2G8A # _model_server_result.job_id lSPXxapfv9P7UYwWImjiQA _model_server_result.datetime_utc '2024-11-23 19:42:01' _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 2g8a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 2G8A # _exptl.entry_id 2G8A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 2G8A _cell.length_a 78.52 _cell.length_b 78.52 _cell.length_c 240.93 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2G8A _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -120.465 # _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 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 358 n n N1 C6 UMP sing 359 n n N1 C1' UMP sing 360 n n C2 N3 UMP sing 361 n n C2 O2 UMP doub 362 n n N3 C4 UMP sing 363 n n N3 HN3 UMP sing 364 n n C4 C5 UMP sing 365 n n C4 O4 UMP doub 366 n n C5 C6 UMP doub 367 n n C5 H5 UMP sing 368 n n C6 H6 UMP sing 369 n n C1' C2' UMP sing 370 n n C1' O4' UMP sing 371 n n C1' H1' UMP sing 372 n n C2' C3' UMP sing 373 n n C2' H2' UMP sing 374 n n C2' "H2''" UMP sing 375 n n C3' C4' UMP sing 376 n n C3' O3' UMP sing 377 n n C3' H3' UMP sing 378 n n C4' O4' UMP sing 379 n n C4' C5' UMP sing 380 n n C4' H4' UMP sing 381 n n O3' HO3' UMP sing 382 n n C5' O5' UMP sing 383 n n C5' H5' UMP sing 384 n n C5' "H5''" UMP sing 385 n n O5' P UMP sing 386 n n P OP1 UMP doub 387 n n P OP2 UMP sing 388 n n P OP3 UMP sing 389 n n OP2 HOP2 UMP sing 390 n n OP3 HOP3 UMP sing 391 n n # _atom_sites.entry_id 2G8A _atom_sites.fract_transf_matrix[1][1] 0.012736 _atom_sites.fract_transf_matrix[1][2] 0.007353 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014706 _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] 0.004151 _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 UMP A 1 317 317 UMP UMP . C 3 HOH A 1 399 399 HOH HOH . C 3 HOH A 2 400 400 HOH HOH . C 3 HOH A 3 401 401 HOH HOH . C 3 HOH A 4 402 402 HOH HOH . C 3 HOH A 5 403 403 HOH HOH . C 3 HOH A 6 404 404 HOH HOH . C 3 HOH A 7 405 405 HOH HOH . C 3 HOH A 8 406 406 HOH HOH . C 3 HOH A 9 407 407 HOH HOH . C 3 HOH A 10 408 408 HOH HOH . C 3 HOH A 11 409 409 HOH HOH . C 3 HOH A 12 410 410 HOH HOH . C 3 HOH A 13 411 411 HOH HOH . C 3 HOH A 14 412 412 HOH HOH . C 3 HOH A 15 413 413 HOH HOH . C 3 HOH A 16 414 414 HOH HOH . C 3 HOH A 17 415 415 HOH HOH . C 3 HOH A 18 416 416 HOH HOH . C 3 HOH A 19 417 417 HOH HOH . C 3 HOH A 20 418 418 HOH HOH . C 3 HOH A 21 420 420 HOH HOH . C 3 HOH A 22 421 421 HOH HOH . C 3 HOH A 23 422 422 HOH HOH . C 3 HOH A 24 423 423 HOH HOH . C 3 HOH A 25 424 424 HOH HOH . C 3 HOH A 26 425 425 HOH HOH . C 3 HOH A 27 426 426 HOH HOH . C 3 HOH A 28 427 427 HOH HOH . C 3 HOH A 29 428 428 HOH HOH . C 3 HOH A 30 429 429 HOH HOH . C 3 HOH A 31 430 430 HOH HOH . C 3 HOH A 32 431 431 HOH HOH . C 3 HOH A 33 432 432 HOH HOH . C 3 HOH A 34 434 434 HOH HOH . C 3 HOH A 35 435 435 HOH HOH . C 3 HOH A 36 436 436 HOH HOH . C 3 HOH A 37 437 437 HOH HOH . C 3 HOH A 38 438 438 HOH HOH . C 3 HOH A 39 439 439 HOH HOH . C 3 HOH A 40 440 440 HOH HOH . C 3 HOH A 41 441 441 HOH HOH . C 3 HOH A 42 442 442 HOH HOH . C 3 HOH A 43 443 443 HOH HOH . C 3 HOH A 44 444 444 HOH HOH . C 3 HOH A 45 445 445 HOH HOH . C 3 HOH A 46 446 446 HOH HOH . C 3 HOH A 47 447 447 HOH HOH . C 3 HOH A 48 448 448 HOH HOH . C 3 HOH A 49 449 449 HOH HOH . C 3 HOH A 50 450 450 HOH HOH . C 3 HOH A 51 451 451 HOH HOH . C 3 HOH A 52 452 452 HOH HOH . C 3 HOH A 53 453 453 HOH HOH . C 3 HOH A 54 457 457 HOH HOH . C 3 HOH A 55 458 458 HOH HOH . C 3 HOH A 56 460 460 HOH HOH . C 3 HOH A 57 465 465 HOH HOH . C 3 HOH A 58 467 467 HOH HOH . C 3 HOH A 59 468 468 HOH HOH . C 3 HOH A 60 469 469 HOH HOH . C 3 HOH A 61 470 470 HOH HOH . C 3 HOH A 62 472 472 HOH HOH . C 3 HOH A 63 473 473 HOH HOH . C 3 HOH A 64 474 474 HOH HOH . C 3 HOH A 65 475 475 HOH HOH . C 3 HOH A 66 476 476 HOH HOH . C 3 HOH A 67 477 477 HOH HOH . C 3 HOH A 68 478 478 HOH HOH . C 3 HOH A 69 479 479 HOH HOH . C 3 HOH A 70 481 481 HOH HOH . C 3 HOH A 71 482 482 HOH HOH . C 3 HOH A 72 483 483 HOH HOH . C 3 HOH A 73 484 484 HOH HOH . C 3 HOH A 74 486 486 HOH HOH . C 3 HOH A 75 491 491 HOH HOH . C 3 HOH A 76 492 492 HOH HOH . C 3 HOH A 77 493 493 HOH HOH . C 3 HOH A 78 496 496 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 N1 UMP . . . B 2 14.593 48.545 -53.634 1 44.29 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 13.729 47.563 -53.128 1 45.52 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 12.793 47.905 -52.138 1 48.71 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 12.729 49.229 -51.612 1 47.17 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 13.596 50.232 -52.104 1 44.84 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 14.514 49.844 -53.113 1 45.67 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 13.743 46.41 -53.551 1 43.02 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 11.897 49.477 -50.727 1 44.91 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 15.579 48.205 -54.691 1 41.19 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 15.058 47.523 -55.951 1 40.19 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 16.066 47.937 -57.046 1 36.95 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 16.454 49.32 -56.595 1 36.14 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 17.192 47.066 -57.154 1 31.3 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 16.24 49.341 -55.183 1 37.48 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 15.637 50.416 -57.338 1 32.53 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 16.499 50.836 -58.409 1 25.1 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 15.816 51.402 -59.75 1 18.54 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 15.279 52.784 -59.652 1 10.84 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 14.686 50.354 -59.743 1 22.54 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 16.69 51.411 -60.894 1 15.44 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #