data_2TSR # _model_server_result.job_id SDSDX2UdXlG5_VaVsRd24A _model_server_result.datetime_utc '2024-12-09 10:16:53' _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 2tsr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":508}' # _entry.id 2TSR # _exptl.entry_id 2TSR _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.4 _cell.angle_gamma 90 _cell.entry_id 2TSR _cell.length_a 99.7 _cell.length_b 101.6 _cell.length_c 140.8 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2TSR _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K N 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 414 n n N1 C6 UMP sing 415 n n N1 C1' UMP sing 416 n n C2 N3 UMP sing 417 n n C2 O2 UMP doub 418 n n N3 C4 UMP sing 419 n n N3 HN3 UMP sing 420 n n C4 C5 UMP sing 421 n n C4 O4 UMP doub 422 n n C5 C6 UMP doub 423 n n C5 H5 UMP sing 424 n n C6 H6 UMP sing 425 n n C1' C2' UMP sing 426 n n C1' O4' UMP sing 427 n n C1' H1' UMP sing 428 n n C2' C3' UMP sing 429 n n C2' H2' UMP sing 430 n n C2' "H2''" UMP sing 431 n n C3' C4' UMP sing 432 n n C3' O3' UMP sing 433 n n C3' H3' UMP sing 434 n n C4' O4' UMP sing 435 n n C4' C5' UMP sing 436 n n C4' H4' UMP sing 437 n n O3' HO3' UMP sing 438 n n C5' O5' UMP sing 439 n n C5' H5' UMP sing 440 n n C5' "H5''" UMP sing 441 n n O5' P UMP sing 442 n n P OP1 UMP doub 443 n n P OP2 UMP sing 444 n n P OP3 UMP sing 445 n n OP2 HOP2 UMP sing 446 n n OP3 HOP3 UMP sing 447 n n # _atom_sites.entry_id 2TSR _atom_sites.fract_transf_matrix[1][1] 0.01003 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002022 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009843 _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] 0.007245 _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 E 2 UMP A 1 308 308 UMP UMP . F 3 D16 A 1 309 309 D16 D16 . G 2 UMP B 1 408 408 UMP UMP . H 3 D16 B 1 409 409 D16 D16 . I 2 UMP C 1 508 508 UMP UMP . J 3 D16 C 1 509 509 D16 D16 . K 2 UMP D 1 608 608 UMP UMP . L 3 D16 D 1 609 609 D16 D16 . M 4 HOH A 1 310 4 HOH HOH . M 4 HOH A 2 311 6 HOH HOH . M 4 HOH A 3 312 8 HOH HOH . M 4 HOH A 4 313 9 HOH HOH . M 4 HOH A 5 314 11 HOH HOH . M 4 HOH A 6 315 12 HOH HOH . M 4 HOH A 7 316 13 HOH HOH . M 4 HOH A 8 317 14 HOH HOH . M 4 HOH A 9 318 15 HOH HOH . M 4 HOH A 10 319 16 HOH HOH . M 4 HOH A 11 320 18 HOH HOH . M 4 HOH A 12 321 23 HOH HOH . M 4 HOH A 13 322 24 HOH HOH . M 4 HOH A 14 323 25 HOH HOH . M 4 HOH A 15 324 26 HOH HOH . M 4 HOH A 16 325 27 HOH HOH . M 4 HOH A 17 326 28 HOH HOH . M 4 HOH A 18 327 29 HOH HOH . M 4 HOH A 19 328 32 HOH HOH . M 4 HOH A 20 329 35 HOH HOH . M 4 HOH A 21 330 36 HOH HOH . M 4 HOH A 22 331 41 HOH HOH . M 4 HOH A 23 332 43 HOH HOH . M 4 HOH A 24 333 46 HOH HOH . N 4 HOH B 1 410 1 HOH HOH . N 4 HOH B 2 411 3 HOH HOH . N 4 HOH B 3 412 5 HOH HOH . N 4 HOH B 4 413 7 HOH HOH . N 4 HOH B 5 414 10 HOH HOH . N 4 HOH B 6 415 17 HOH HOH . N 4 HOH B 7 416 19 HOH HOH . N 4 HOH B 8 417 20 HOH HOH . N 4 HOH B 9 418 21 HOH HOH . N 4 HOH B 10 419 22 HOH HOH . N 4 HOH B 11 420 30 HOH HOH . N 4 HOH B 12 421 31 HOH HOH . N 4 HOH B 13 422 33 HOH HOH . N 4 HOH B 14 423 34 HOH HOH . N 4 HOH B 15 424 37 HOH HOH . N 4 HOH B 16 425 38 HOH HOH . N 4 HOH B 17 426 39 HOH HOH . N 4 HOH B 18 427 40 HOH HOH . N 4 HOH B 19 428 42 HOH HOH . N 4 HOH B 20 429 44 HOH HOH . N 4 HOH B 21 430 45 HOH HOH . N 4 HOH B 22 431 47 HOH HOH . N 4 HOH B 23 432 48 HOH HOH . N 4 HOH B 24 433 50 HOH HOH . N 4 HOH B 25 434 55 HOH HOH . N 4 HOH B 26 435 57 HOH HOH . O 4 HOH C 1 510 2 HOH HOH . O 4 HOH C 2 511 61 HOH HOH . O 4 HOH C 3 512 64 HOH HOH . O 4 HOH C 4 513 67 HOH HOH . O 4 HOH C 5 514 68 HOH HOH . O 4 HOH C 6 515 69 HOH HOH . O 4 HOH C 7 516 71 HOH HOH . O 4 HOH C 8 517 72 HOH HOH . O 4 HOH C 9 518 74 HOH HOH . P 4 HOH D 1 610 49 HOH HOH . P 4 HOH D 2 611 51 HOH HOH . P 4 HOH D 3 612 52 HOH HOH . P 4 HOH D 4 613 53 HOH HOH . P 4 HOH D 5 614 54 HOH HOH . P 4 HOH D 6 615 56 HOH HOH . P 4 HOH D 7 616 58 HOH HOH . P 4 HOH D 8 617 59 HOH HOH . P 4 HOH D 9 618 60 HOH HOH . P 4 HOH D 10 619 62 HOH HOH . P 4 HOH D 11 620 63 HOH HOH . P 4 HOH D 12 621 65 HOH HOH . P 4 HOH D 13 622 66 HOH HOH . P 4 HOH D 14 623 70 HOH HOH . P 4 HOH D 15 624 73 HOH HOH . P 4 HOH D 16 625 75 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 . . . I 2 19.69 -25.786 65.869 1 51.59 ? N1 UMP 508 C 1 HETATM 2 C C2 UMP . . . I 2 18.904 -26.649 65.118 1 47.84 ? C2 UMP 508 C 1 HETATM 3 N N3 UMP . . . I 2 17.675 -26.919 65.67 1 42.06 ? N3 UMP 508 C 1 HETATM 4 C C4 UMP . . . I 2 17.161 -26.42 66.855 1 47.32 ? C4 UMP 508 C 1 HETATM 5 C C5 UMP . . . I 2 18.02 -25.51 67.542 1 52.78 ? C5 UMP 508 C 1 HETATM 6 C C6 UMP . . . I 2 19.219 -25.231 67.04 1 52.96 ? C6 UMP 508 C 1 HETATM 7 O O2 UMP . . . I 2 19.26 -27.138 64.052 1 44.81 ? O2 UMP 508 C 1 HETATM 8 O O4 UMP . . . I 2 16.074 -26.825 67.263 1 52.78 ? O4 UMP 508 C 1 HETATM 9 C C1' UMP . . . I 2 21.066 -25.483 65.434 1 58.34 ? C1' UMP 508 C 1 HETATM 10 C C2' UMP . . . I 2 21.397 -25.379 63.944 1 61.29 ? C2' UMP 508 C 1 HETATM 11 C C3' UMP . . . I 2 21.625 -23.879 63.767 1 62.97 ? C3' UMP 508 C 1 HETATM 12 C C4' UMP . . . I 2 22.097 -23.402 65.139 1 62.53 ? C4' UMP 508 C 1 HETATM 13 O O3' UMP . . . I 2 22.671 -23.58 62.833 1 64.75 ? O3' UMP 508 C 1 HETATM 14 O O4' UMP . . . I 2 21.472 -24.294 66.087 1 62.63 ? O4' UMP 508 C 1 HETATM 15 C C5' UMP . . . I 2 21.704 -21.978 65.515 1 63.04 ? C5' UMP 508 C 1 HETATM 16 O O5' UMP . . . I 2 22.313 -21.006 64.629 1 61.17 ? O5' UMP 508 C 1 HETATM 17 P P UMP . . . I 2 21.434 -19.807 63.942 1 40.92 ? P UMP 508 C 1 HETATM 18 O OP1 UMP . . . I 2 22.445 -18.789 63.448 1 44.87 ? OP1 UMP 508 C 1 HETATM 19 O OP2 UMP . . . I 2 20.68 -20.48 62.814 1 42.11 ? OP2 UMP 508 C 1 HETATM 20 O OP3 UMP . . . I 2 20.518 -19.235 65.012 1 41.57 ? OP3 UMP 508 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 62 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #