data_1TVV
#
_model_server_result.job_id            pKX8aX0UsCP-wH7uyGodhQ 
_model_server_result.datetime_utc      '2024-11-23 23:40:28' 
_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          1tvv 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":317}' 
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_entry.id    1TVV 
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_exptl.entry_id    1TVV 
_exptl.method      'X-RAY DIFFRACTION' 
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_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            1TVV 
_cell.length_a            78.7 
_cell.length_b            78.7 
_cell.length_c            230.7 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 1TVV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61 2 2' 
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_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 
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_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
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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 -115.35 
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_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 418 n n 
N1 C6 UMP sing 419 n n 
N1 C1' UMP sing 420 n n 
C2 N3 UMP sing 421 n n 
C2 O2 UMP doub 422 n n 
N3 C4 UMP sing 423 n n 
N3 HN3 UMP sing 424 n n 
C4 C5 UMP sing 425 n n 
C4 O4 UMP doub 426 n n 
C5 C6 UMP doub 427 n n 
C5 H5 UMP sing 428 n n 
C6 H6 UMP sing 429 n n 
C1' C2' UMP sing 430 n n 
C1' O4' UMP sing 431 n n 
C1' H1' UMP sing 432 n n 
C2' C3' UMP sing 433 n n 
C2' H2' UMP sing 434 n n 
C2' "H2''" UMP sing 435 n n 
C3' C4' UMP sing 436 n n 
C3' O3' UMP sing 437 n n 
C3' H3' UMP sing 438 n n 
C4' O4' UMP sing 439 n n 
C4' C5' UMP sing 440 n n 
C4' H4' UMP sing 441 n n 
O3' HO3' UMP sing 442 n n 
C5' O5' UMP sing 443 n n 
C5' H5' UMP sing 444 n n 
C5' "H5''" UMP sing 445 n n 
O5' P UMP sing 446 n n 
P OP1 UMP doub 447 n n 
P OP2 UMP sing 448 n n 
P OP3 UMP sing 449 n n 
OP2 HOP2 UMP sing 450 n n 
OP3 HOP3 UMP sing 451 n n 
#
_atom_sites.entry_id                     1TVV 
_atom_sites.fract_transf_matrix[1][1]    0.012706 
_atom_sites.fract_transf_matrix[1][2]    0.007336 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014672 
_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]    0.004335 
_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 CB3 A 1 318 318 CB3 CB3 . 
D 4 HOH A 1 319 319 HOH HOH . 
D 4 HOH A 2 320 320 HOH HOH . 
D 4 HOH A 3 321 321 HOH HOH . 
D 4 HOH A 4 322 322 HOH HOH . 
D 4 HOH A 5 323 323 HOH HOH . 
D 4 HOH A 6 324 324 HOH HOH . 
D 4 HOH A 7 325 325 HOH HOH . 
D 4 HOH A 8 326 326 HOH HOH . 
D 4 HOH A 9 327 327 HOH HOH . 
D 4 HOH A 10 328 328 HOH HOH . 
D 4 HOH A 11 329 329 HOH HOH . 
D 4 HOH A 12 330 330 HOH HOH . 
D 4 HOH A 13 331 331 HOH HOH . 
D 4 HOH A 14 332 332 HOH HOH . 
D 4 HOH A 15 333 333 HOH HOH . 
D 4 HOH A 16 334 334 HOH HOH . 
D 4 HOH A 17 335 335 HOH HOH . 
D 4 HOH A 18 336 336 HOH HOH . 
D 4 HOH A 19 337 337 HOH HOH . 
D 4 HOH A 20 338 338 HOH HOH . 
D 4 HOH A 21 339 339 HOH HOH . 
D 4 HOH A 22 340 340 HOH HOH . 
D 4 HOH A 23 341 341 HOH HOH . 
D 4 HOH A 24 342 342 HOH HOH . 
D 4 HOH A 25 343 343 HOH HOH . 
D 4 HOH A 26 344 344 HOH HOH . 
D 4 HOH A 27 345 345 HOH HOH . 
D 4 HOH A 28 346 346 HOH HOH . 
D 4 HOH A 29 347 347 HOH HOH . 
D 4 HOH A 30 348 348 HOH HOH . 
D 4 HOH A 31 349 349 HOH HOH . 
D 4 HOH A 32 350 350 HOH HOH . 
D 4 HOH A 33 351 351 HOH HOH . 
D 4 HOH A 34 352 352 HOH HOH . 
D 4 HOH A 35 353 353 HOH HOH . 
D 4 HOH A 36 354 354 HOH HOH . 
D 4 HOH A 37 356 356 HOH HOH . 
D 4 HOH A 38 359 359 HOH HOH . 
D 4 HOH A 39 369 369 HOH HOH . 
D 4 HOH A 40 373 373 HOH HOH . 
D 4 HOH A 41 374 374 HOH HOH . 
D 4 HOH A 42 376 376 HOH HOH . 
D 4 HOH A 43 378 378 HOH HOH . 
D 4 HOH A 44 380 380 HOH HOH . 
D 4 HOH A 45 383 383 HOH HOH . 
D 4 HOH A 46 389 389 HOH HOH . 
D 4 HOH A 47 390 390 HOH HOH . 
D 4 HOH A 48 400 400 HOH HOH . 
D 4 HOH A 49 402 402 HOH HOH . 
D 4 HOH A 50 405 405 HOH HOH . 
D 4 HOH A 51 406 406 HOH HOH . 
D 4 HOH A 52 407 407 HOH HOH . 
D 4 HOH A 53 413 413 HOH HOH . 
D 4 HOH A 54 414 414 HOH HOH . 
D 4 HOH A 55 415 415 HOH HOH . 
D 4 HOH A 56 416 416 HOH HOH . 
D 4 HOH A 57 417 417 HOH HOH . 
D 4 HOH A 58 418 418 HOH HOH . 
D 4 HOH A 59 419 419 HOH HOH . 
D 4 HOH A 60 425 425 HOH HOH . 
D 4 HOH A 61 426 426 HOH HOH . 
D 4 HOH A 62 428 428 HOH HOH . 
D 4 HOH A 63 429 429 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 14.901 46.76 -52.155 1 60.28 ? N1 UMP 317 A 1 
HETATM 2 C C2 UMP . . . B 2 14.556 45.424 -51.957 1 60.97 ? C2 UMP 317 A 1 
HETATM 3 N N3 UMP . . . B 2 13.665 45.077 -50.991 1 60.97 ? N3 UMP 317 A 1 
HETATM 4 C C4 UMP . . . B 2 13.054 45.973 -50.165 1 62.82 ? C4 UMP 317 A 1 
HETATM 5 C C5 UMP . . . B 2 13.453 47.397 -50.364 1 62.49 ? C5 UMP 317 A 1 
HETATM 6 C C6 UMP . . . B 2 14.389 47.741 -51.381 1 62.04 ? C6 UMP 317 A 1 
HETATM 7 O O2 UMP . . . B 2 15.042 44.517 -52.606 1 61.12 ? O2 UMP 317 A 1 
HETATM 8 O O4 UMP . . . B 2 12.2 45.485 -49.418 1 65.23 ? O4 UMP 317 A 1 
HETATM 9 C C1' UMP . . . B 2 15.806 46.939 -53.371 1 58.15 ? C1' UMP 317 A 1 
HETATM 10 C C2' UMP . . . B 2 15.152 46.698 -54.74 1 54.35 ? C2' UMP 317 A 1 
HETATM 11 C C3' UMP . . . B 2 16.331 46.831 -55.694 1 53.04 ? C3' UMP 317 A 1 
HETATM 12 C C4' UMP . . . B 2 17.114 48.059 -55.22 1 50.39 ? C4' UMP 317 A 1 
HETATM 13 O O3' UMP . . . B 2 17.194 45.663 -55.553 1 51.51 ? O3' UMP 317 A 1 
HETATM 14 O O4' UMP . . . B 2 16.686 48.107 -53.763 1 55.9 ? O4' UMP 317 A 1 
HETATM 15 C C5' UMP . . . B 2 16.588 49.321 -55.886 1 45.48 ? C5' UMP 317 A 1 
HETATM 16 O O5' UMP . . . B 2 16.935 49.252 -57.282 1 41.25 ? O5' UMP 317 A 1 
HETATM 17 P P UMP . . . B 2 15.832 49.543 -58.377 1 32.55 ? P UMP 317 A 1 
HETATM 18 O OP1 UMP . . . B 2 16.507 49.611 -59.675 1 33.02 ? OP1 UMP 317 A 1 
HETATM 19 O OP2 UMP . . . B 2 14.86 48.449 -58.336 1 35.46 ? OP2 UMP 317 A 1 
HETATM 20 O OP3 UMP . . . B 2 15.201 50.832 -58.052 1 31.38 ? OP3 UMP 317 A 1 
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_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           239 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
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