data_3HB8
#
_model_server_result.job_id            12rmRcVkyKF6AxA-RxdBng 
_model_server_result.datetime_utc      '2024-11-27 17:28:27' 
_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":"J","auth_seq_id":365}' 
#
_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 . . . J 2 -6.905 -79.742 35.371 0.39 62.09 ? N1 UMP 365 C 1 
HETATM 2 C C2 UMP . . . J 2 -5.71 -79.212 35.854 0.39 63.47 ? C2 UMP 365 C 1 
HETATM 3 N N3 UMP . . . J 2 -5.433 -79.248 37.194 0.39 63.61 ? N3 UMP 365 C 1 
HETATM 4 C C4 UMP . . . J 2 -6.318 -79.816 38.078 0.39 61.63 ? C4 UMP 365 C 1 
HETATM 5 C C5 UMP . . . J 2 -7.549 -80.371 37.608 0.39 61.36 ? C5 UMP 365 C 1 
HETATM 6 C C6 UMP . . . J 2 -7.822 -80.33 36.261 0.39 61.41 ? C6 UMP 365 C 1 
HETATM 7 O O2 UMP . . . J 2 -4.901 -78.698 35.091 0.39 63.68 ? O2 UMP 365 C 1 
HETATM 8 O O4 UMP . . . J 2 -6.061 -79.845 39.257 0.39 60.14 ? O4 UMP 365 C 1 
HETATM 9 C C1' UMP . . . J 2 -7.194 -79.694 33.916 0.39 58.21 ? C1' UMP 365 C 1 
HETATM 10 C C2' UMP . . . J 2 -7.188 -81.111 33.29 0.39 57.34 ? C2' UMP 365 C 1 
HETATM 11 C C3' UMP . . . J 2 -8.206 -80.999 32.134 0.39 53.88 ? C3' UMP 365 C 1 
HETATM 12 C C4' UMP . . . J 2 -8.663 -79.53 32.21 0.39 51.88 ? C4' UMP 365 C 1 
HETATM 13 O O3' UMP . . . J 2 -7.553 -81.26 30.881 0.39 53.36 ? O3' UMP 365 C 1 
HETATM 14 O O4' UMP . . . J 2 -8.507 -79.189 33.613 0.39 54.11 ? O4' UMP 365 C 1 
HETATM 15 C C5' UMP . . . J 2 -10.108 -79.379 31.738 0.39 46 ? C5' UMP 365 C 1 
HETATM 16 O O5' UMP . . . J 2 -10.502 -78.007 31.83 0.39 35.56 ? O5' UMP 365 C 1 
HETATM 17 P P UMP . . . J 2 -12.021 -77.886 31.31 0.39 29.45 ? P UMP 365 C 1 
HETATM 18 O OP1 UMP . . . J 2 -12.906 -78.742 32.12 0.39 27.35 ? OP1 UMP 365 C 1 
HETATM 19 O OP2 UMP . . . J 2 -12.504 -76.359 31.419 0.39 24.68 ? OP2 UMP 365 C 1 
HETATM 20 O OP3 UMP . . . J 2 -12.08 -78.338 29.771 0.39 26.16 ? OP3 UMP 365 C 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           261 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#