data_3HB8 # _model_server_result.job_id ySjh_On30bkD-8S1NqdROQ _model_server_result.datetime_utc '2024-11-23 23:40:24' _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 3hb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":565}' # _entry.id 3HB8 # _exptl.entry_id 3HB8 _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 114.55 _cell.angle_gamma 90 _cell.entry_id 3HB8 _cell.length_a 196.459 _cell.length_b 122.149 _cell.length_c 99.157 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HB8 _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 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,F,G,H,I,N,O 1 1 C,J,P 2 1,2 D,E,K,L,M,Q,R 3 1 # 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_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -41.198462 0 90.193112 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 F N N ? 2 J 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 371 n n N1 C6 UMP sing 372 n n N1 C1' UMP sing 373 n n C2 N3 UMP sing 374 n n C2 O2 UMP doub 375 n n N3 C4 UMP sing 376 n n N3 HN3 UMP sing 377 n n C4 C5 UMP sing 378 n n C4 O4 UMP doub 379 n n C5 C6 UMP doub 380 n n C5 H5 UMP sing 381 n n C6 H6 UMP sing 382 n n C1' C2' UMP sing 383 n n C1' O4' UMP sing 384 n n C1' H1' UMP sing 385 n n C2' C3' UMP sing 386 n n C2' H2' UMP sing 387 n n C2' "H2''" UMP sing 388 n n C3' C4' UMP sing 389 n n C3' O3' UMP sing 390 n n C3' H3' UMP sing 391 n n C4' O4' UMP sing 392 n n C4' C5' UMP sing 393 n n C4' H4' UMP sing 394 n n O3' HO3' UMP sing 395 n n C5' O5' UMP sing 396 n n C5' H5' UMP sing 397 n n C5' "H5''" UMP sing 398 n n O5' P UMP sing 399 n n P OP1 UMP doub 400 n n P OP2 UMP sing 401 n n P OP3 UMP sing 402 n n OP2 HOP2 UMP sing 403 n n OP3 HOP3 UMP sing 404 n n # _atom_sites.entry_id 3HB8 _atom_sites.fract_transf_matrix[1][1] 0.00509 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002325 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008187 _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] 0.011087 _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 F 2 UMP A 1 314 165 UMP UMP . G 3 EDO A 1 315 114 EDO EDO . H 4 PO4 B 1 615 615 PO4 PO4 . I 3 EDO B 1 314 214 EDO EDO . J 2 UMP C 1 365 365 UMP UMP . K 2 UMP D 1 565 565 UMP UMP . L 4 PO4 D 1 616 616 PO4 PO4 . M 3 EDO E 1 614 614 EDO EDO . N 5 HOH A 1 316 2 HOH HOH . N 5 HOH A 2 317 6 HOH HOH . N 5 HOH A 3 318 7 HOH HOH . N 5 HOH A 4 319 14 HOH HOH . N 5 HOH A 5 320 16 HOH HOH . N 5 HOH A 6 321 17 HOH HOH . N 5 HOH A 7 322 19 HOH HOH . N 5 HOH A 8 323 20 HOH HOH . N 5 HOH A 9 324 22 HOH HOH . N 5 HOH A 10 325 33 HOH HOH . N 5 HOH A 11 326 34 HOH HOH . N 5 HOH A 12 327 43 HOH HOH . N 5 HOH A 13 328 51 HOH HOH . N 5 HOH A 14 329 53 HOH HOH . N 5 HOH A 15 330 60 HOH HOH . N 5 HOH A 16 331 61 HOH HOH . N 5 HOH A 17 332 62 HOH HOH . N 5 HOH A 18 333 73 HOH HOH . N 5 HOH A 19 334 82 HOH HOH . N 5 HOH A 20 335 83 HOH HOH . N 5 HOH A 21 336 86 HOH HOH . N 5 HOH A 22 337 89 HOH HOH . N 5 HOH A 23 338 93 HOH HOH . N 5 HOH A 24 339 94 HOH HOH . N 5 HOH A 25 340 107 HOH HOH . N 5 HOH A 26 341 110 HOH HOH . N 5 HOH A 27 342 113 HOH HOH . N 5 HOH A 28 343 118 HOH HOH . N 5 HOH A 29 344 119 HOH HOH . N 5 HOH A 30 345 120 HOH HOH . N 5 HOH A 31 346 121 HOH HOH . N 5 HOH A 32 347 123 HOH HOH . O 5 HOH B 1 315 3 HOH HOH . O 5 HOH B 2 316 4 HOH HOH . O 5 HOH B 3 317 11 HOH HOH . O 5 HOH B 4 318 12 HOH HOH . O 5 HOH B 5 319 13 HOH HOH . O 5 HOH B 6 320 23 HOH HOH . O 5 HOH B 7 321 30 HOH HOH . O 5 HOH B 8 322 47 HOH HOH . O 5 HOH B 9 323 52 HOH HOH . O 5 HOH B 10 324 58 HOH HOH . O 5 HOH B 11 325 65 HOH HOH . O 5 HOH B 12 326 84 HOH HOH . O 5 HOH B 13 327 117 HOH HOH . O 5 HOH B 14 328 125 HOH HOH . P 5 HOH C 1 314 5 HOH HOH . P 5 HOH C 2 315 8 HOH HOH . P 5 HOH C 3 316 9 HOH HOH . P 5 HOH C 4 317 21 HOH HOH . P 5 HOH C 5 318 25 HOH HOH . P 5 HOH C 6 319 28 HOH HOH . P 5 HOH C 7 320 29 HOH HOH . P 5 HOH C 8 321 31 HOH HOH . P 5 HOH C 9 322 32 HOH HOH . P 5 HOH C 10 323 36 HOH HOH . P 5 HOH C 11 324 37 HOH HOH . P 5 HOH C 12 325 45 HOH HOH . P 5 HOH C 13 326 46 HOH HOH . P 5 HOH C 14 327 49 HOH HOH . P 5 HOH C 15 328 54 HOH HOH . P 5 HOH C 16 329 55 HOH HOH . P 5 HOH C 17 330 71 HOH HOH . P 5 HOH C 18 331 81 HOH HOH . P 5 HOH C 19 332 85 HOH HOH . P 5 HOH C 20 333 87 HOH HOH . P 5 HOH C 21 334 90 HOH HOH . P 5 HOH C 22 335 92 HOH HOH . P 5 HOH C 23 336 95 HOH HOH . P 5 HOH C 24 337 97 HOH HOH . P 5 HOH C 25 338 105 HOH HOH . P 5 HOH C 26 339 106 HOH HOH . P 5 HOH C 27 340 109 HOH HOH . P 5 HOH C 28 341 112 HOH HOH . P 5 HOH C 29 342 114 HOH HOH . P 5 HOH C 30 343 116 HOH HOH . P 5 HOH C 31 344 124 HOH HOH . P 5 HOH C 32 345 126 HOH HOH . Q 5 HOH D 1 314 15 HOH HOH . Q 5 HOH D 2 315 35 HOH HOH . Q 5 HOH D 3 316 38 HOH HOH . Q 5 HOH D 4 317 41 HOH HOH . Q 5 HOH D 5 318 50 HOH HOH . Q 5 HOH D 6 319 57 HOH HOH . Q 5 HOH D 7 320 67 HOH HOH . Q 5 HOH D 8 321 69 HOH HOH . Q 5 HOH D 9 322 75 HOH HOH . Q 5 HOH D 10 323 76 HOH HOH . Q 5 HOH D 11 324 88 HOH HOH . Q 5 HOH D 12 325 91 HOH HOH . Q 5 HOH D 13 326 101 HOH HOH . Q 5 HOH D 14 327 103 HOH HOH . Q 5 HOH D 15 328 104 HOH HOH . Q 5 HOH D 16 329 111 HOH HOH . Q 5 HOH D 17 330 122 HOH HOH . Q 5 HOH D 18 331 127 HOH HOH . Q 5 HOH D 19 332 128 HOH HOH . R 5 HOH E 1 314 1 HOH HOH . R 5 HOH E 2 315 10 HOH HOH . R 5 HOH E 3 316 18 HOH HOH . R 5 HOH E 4 317 24 HOH HOH . R 5 HOH E 5 318 26 HOH HOH . R 5 HOH E 6 319 27 HOH HOH . R 5 HOH E 7 320 39 HOH HOH . R 5 HOH E 8 321 40 HOH HOH . R 5 HOH E 9 322 42 HOH HOH . R 5 HOH E 10 323 44 HOH HOH . R 5 HOH E 11 324 48 HOH HOH . R 5 HOH E 12 325 56 HOH HOH . R 5 HOH E 13 326 59 HOH HOH . R 5 HOH E 14 327 63 HOH HOH . R 5 HOH E 15 328 64 HOH HOH . R 5 HOH E 16 329 66 HOH HOH . R 5 HOH E 17 330 68 HOH HOH . R 5 HOH E 18 331 70 HOH HOH . R 5 HOH E 19 332 72 HOH HOH . R 5 HOH E 20 333 78 HOH HOH . R 5 HOH E 21 334 79 HOH HOH . R 5 HOH E 22 335 80 HOH HOH . R 5 HOH E 23 336 96 HOH HOH . R 5 HOH E 24 337 98 HOH HOH . R 5 HOH E 25 338 100 HOH HOH . R 5 HOH E 26 339 102 HOH HOH . R 5 HOH E 27 340 115 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 . . . K 2 19.877 -15.911 56.461 0.87 100.11 ? N1 UMP 565 D 1 HETATM 2 C C2 UMP . . . K 2 21.028 -15.217 56.121 0.87 102.78 ? C2 UMP 565 D 1 HETATM 3 N N3 UMP . . . K 2 21.373 -15.055 54.807 0.87 103.17 ? N3 UMP 565 D 1 HETATM 4 C C4 UMP . . . K 2 20.589 -15.571 53.809 0.87 103.3 ? C4 UMP 565 D 1 HETATM 5 C C5 UMP . . . K 2 19.394 -16.288 54.138 0.87 102.43 ? C5 UMP 565 D 1 HETATM 6 C C6 UMP . . . K 2 19.061 -16.444 55.456 0.87 100.81 ? C6 UMP 565 D 1 HETATM 7 O O2 UMP . . . K 2 21.756 -14.745 56.986 0.87 103.98 ? O2 UMP 565 D 1 HETATM 8 O O4 UMP . . . K 2 20.909 -15.42 52.647 0.87 103.22 ? O4 UMP 565 D 1 HETATM 9 C C1' UMP . . . K 2 19.517 -16.094 57.9 0.87 95.79 ? C1' UMP 565 D 1 HETATM 10 C C2' UMP . . . K 2 18.023 -15.829 58.215 0.87 92.4 ? C2' UMP 565 D 1 HETATM 11 C C3' UMP . . . K 2 17.727 -16.815 59.38 0.87 89.66 ? C3' UMP 565 D 1 HETATM 12 C C4' UMP . . . K 2 19.075 -17.54 59.607 0.87 87.87 ? C4' UMP 565 D 1 HETATM 13 O O3' UMP . . . K 2 17.361 -16.091 60.564 0.87 83.81 ? O3' UMP 565 D 1 HETATM 14 O O4' UMP . . . K 2 19.745 -17.451 58.329 0.87 91.9 ? O4' UMP 565 D 1 HETATM 15 C C5' UMP . . . K 2 18.86 -19.012 60.012 0.87 82.05 ? C5' UMP 565 D 1 HETATM 16 O O5' UMP . . . K 2 20.131 -19.657 60.209 0.87 70.89 ? O5' UMP 565 D 1 HETATM 17 P P UMP . . . K 2 19.879 -21.193 60.645 1 63.5 ? P UMP 565 D 1 HETATM 18 O OP1 UMP . . . K 2 19.103 -21.902 59.618 1 63.48 ? OP1 UMP 565 D 1 HETATM 19 O OP2 UMP . . . K 2 21.296 -21.916 60.859 1 67.07 ? OP2 UMP 565 D 1 HETATM 20 O OP3 UMP . . . K 2 19.078 -21.231 62.031 1 67.38 ? OP3 UMP 565 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #