data_1JMH # _model_server_result.job_id UJAFekKt6-tkSlHK1cWrew _model_server_result.datetime_utc '2024-11-24 00:42:38' _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 1jmh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 1JMH # _exptl.entry_id 1JMH _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 1JMH _cell.length_a 78.4 _cell.length_b 78.4 _cell.length_c 242.5 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JMH _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 -121.25 # _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 1JMH _atom_sites.fract_transf_matrix[1][1] 0.012755 _atom_sites.fract_transf_matrix[1][2] 0.007364 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014728 _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] 0.004124 _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 1 318 318 HOH HOH . C 3 HOH A 2 321 321 HOH HOH . C 3 HOH A 3 322 322 HOH HOH . C 3 HOH A 4 323 323 HOH HOH . C 3 HOH A 5 324 324 HOH HOH . C 3 HOH A 6 325 325 HOH HOH . C 3 HOH A 7 326 326 HOH HOH . C 3 HOH A 8 327 327 HOH HOH . C 3 HOH A 9 328 328 HOH HOH . C 3 HOH A 10 329 329 HOH HOH . C 3 HOH A 11 330 330 HOH HOH . C 3 HOH A 12 331 331 HOH HOH . C 3 HOH A 13 335 335 HOH HOH . C 3 HOH A 14 339 339 HOH HOH . C 3 HOH A 15 340 340 HOH HOH . C 3 HOH A 16 343 343 HOH HOH . C 3 HOH A 17 344 344 HOH HOH . C 3 HOH A 18 348 348 HOH HOH . C 3 HOH A 19 350 350 HOH HOH . C 3 HOH A 20 351 351 HOH HOH . C 3 HOH A 21 353 353 HOH HOH . C 3 HOH A 22 354 354 HOH HOH . C 3 HOH A 23 359 359 HOH HOH . C 3 HOH A 24 360 360 HOH HOH . C 3 HOH A 25 362 362 HOH HOH . C 3 HOH A 26 364 364 HOH HOH . C 3 HOH A 27 365 365 HOH HOH . C 3 HOH A 28 368 368 HOH HOH . C 3 HOH A 29 370 370 HOH HOH . C 3 HOH A 30 373 373 HOH HOH . C 3 HOH A 31 375 375 HOH HOH . C 3 HOH A 32 379 379 HOH HOH . C 3 HOH A 33 386 386 HOH HOH . C 3 HOH A 34 387 387 HOH HOH . C 3 HOH A 35 390 390 HOH HOH . C 3 HOH A 36 392 392 HOH HOH . C 3 HOH A 37 406 406 HOH HOH . C 3 HOH A 38 408 408 HOH HOH . C 3 HOH A 39 410 410 HOH HOH . C 3 HOH A 40 411 411 HOH HOH . C 3 HOH A 41 418 418 HOH HOH . C 3 HOH A 42 420 420 HOH HOH . C 3 HOH A 43 425 425 HOH HOH . C 3 HOH A 44 429 429 HOH HOH . C 3 HOH A 45 436 436 HOH HOH . C 3 HOH A 46 437 437 HOH HOH . C 3 HOH A 47 439 439 HOH HOH . C 3 HOH A 48 443 443 HOH HOH . C 3 HOH A 49 444 444 HOH HOH . C 3 HOH A 50 449 449 HOH HOH . C 3 HOH A 51 452 452 HOH HOH . C 3 HOH A 52 453 453 HOH HOH . C 3 HOH A 53 456 456 HOH HOH . C 3 HOH A 54 458 458 HOH HOH . C 3 HOH A 55 460 460 HOH HOH . C 3 HOH A 56 461 461 HOH HOH . C 3 HOH A 57 464 464 HOH HOH . C 3 HOH A 58 466 466 HOH HOH . C 3 HOH A 59 467 467 HOH HOH . C 3 HOH A 60 468 468 HOH HOH . C 3 HOH A 61 470 470 HOH HOH . C 3 HOH A 62 481 481 HOH HOH . C 3 HOH A 63 482 482 HOH HOH . C 3 HOH A 64 483 483 HOH HOH . C 3 HOH A 65 484 484 HOH HOH . C 3 HOH A 66 485 485 HOH HOH . C 3 HOH A 67 486 486 HOH HOH . C 3 HOH A 68 488 488 HOH HOH . C 3 HOH A 69 490 490 HOH HOH . C 3 HOH A 70 494 494 HOH HOH . C 3 HOH A 71 496 496 HOH HOH . C 3 HOH A 72 499 499 HOH HOH . C 3 HOH A 73 502 502 HOH HOH . C 3 HOH A 74 506 506 HOH HOH . C 3 HOH A 75 509 509 HOH HOH . C 3 HOH A 76 512 512 HOH HOH . C 3 HOH A 77 514 514 HOH HOH . C 3 HOH A 78 515 515 HOH HOH . C 3 HOH A 79 516 516 HOH HOH . C 3 HOH A 80 517 517 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 15.172 48.733 -53.662 1 78.48 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 14.31 47.649 -53.333 1 79.25 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 14.052 47.493 -51.982 1 81.07 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 14.562 48.29 -50.961 1 82.73 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 15.411 49.388 -51.395 1 81.41 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 15.671 49.562 -52.751 1 79.65 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 13.765 46.864 -54.11 1 77.05 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 14.303 48.028 -49.787 1 84.88 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 15.884 48.869 -54.963 1 74.82 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 15.183 48.473 -56.264 1 71.78 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 16.305 48.709 -57.264 1 68.89 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 16.895 50.09 -56.929 1 66.71 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 17.304 47.693 -56.97 1 66.5 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 16.511 50.158 -55.456 1 70.82 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 16.194 51.192 -57.739 1 57.71 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 16.591 51.156 -59.174 1 43.4 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 15.826 51.974 -60.302 1 29.43 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 14.537 51.304 -60.376 1 36.31 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 15.619 53.367 -59.862 1 33.33 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 16.42 51.97 -61.654 1 26.71 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #