data_3N0C
#
_model_server_result.job_id            HUqyZo6_H4k_IVWcciTTVA 
_model_server_result.datetime_utc      '2025-07-07 18:58:01' 
_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          3n0c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":318}' 
#
_entry.id    3N0C 
#
_exptl.entry_id    3N0C 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            3N0C 
_cell.length_a            54.549 
_cell.length_b            116.718 
_cell.length_c            141.202 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3N0C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 J N N 
? 2 L 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 449 n n 
N1 C6 UMP sing 450 n n 
N1 C1' UMP sing 451 n n 
C2 N3 UMP sing 452 n n 
C2 O2 UMP doub 453 n n 
N3 C4 UMP sing 454 n n 
N3 HN3 UMP sing 455 n n 
C4 C5 UMP sing 456 n n 
C4 O4 UMP doub 457 n n 
C5 C6 UMP doub 458 n n 
C5 H5 UMP sing 459 n n 
C6 H6 UMP sing 460 n n 
C1' C2' UMP sing 461 n n 
C1' O4' UMP sing 462 n n 
C1' H1' UMP sing 463 n n 
C2' C3' UMP sing 464 n n 
C2' H2' UMP sing 465 n n 
C2' "H2''" UMP sing 466 n n 
C3' C4' UMP sing 467 n n 
C3' O3' UMP sing 468 n n 
C3' H3' UMP sing 469 n n 
C4' O4' UMP sing 470 n n 
C4' C5' UMP sing 471 n n 
C4' H4' UMP sing 472 n n 
O3' HO3' UMP sing 473 n n 
C5' O5' UMP sing 474 n n 
C5' H5' UMP sing 475 n n 
C5' "H5''" UMP sing 476 n n 
O5' P UMP sing 477 n n 
P OP1 UMP doub 478 n n 
P OP2 UMP sing 479 n n 
P OP3 UMP sing 480 n n 
OP2 HOP2 UMP sing 481 n n 
OP3 HOP3 UMP sing 482 n n 
#
_atom_sites.entry_id                     3N0C 
_atom_sites.fract_transf_matrix[1][1]    0.018332 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008568 
_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]    0.007082 
_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 1 303 303 UMP UMP . 
F 3 FAD A 1 315 315 FAD FAD . 
G 2 UMP B 1 308 308 UMP UMP . 
H 3 FAD B 1 310 310 FAD FAD . 
I 3 FAD C 1 305 305 FAD FAD . 
J 2 UMP C 1 313 313 UMP UMP . 
K 3 FAD D 1 300 300 FAD FAD . 
L 2 UMP D 1 318 318 UMP UMP . 
M 4 HOH A 1 221 4 HOH HOH . 
M 4 HOH A 2 222 14 HOH HOH . 
M 4 HOH A 3 223 17 HOH HOH . 
M 4 HOH A 4 224 21 HOH HOH . 
M 4 HOH A 5 225 22 HOH HOH . 
M 4 HOH A 6 226 25 HOH HOH . 
M 4 HOH A 7 227 27 HOH HOH . 
M 4 HOH A 8 228 28 HOH HOH . 
M 4 HOH A 9 229 30 HOH HOH . 
M 4 HOH A 10 230 32 HOH HOH . 
M 4 HOH A 11 231 40 HOH HOH . 
N 4 HOH B 1 221 3 HOH HOH . 
N 4 HOH B 2 222 6 HOH HOH . 
N 4 HOH B 3 223 7 HOH HOH . 
N 4 HOH B 4 224 11 HOH HOH . 
N 4 HOH B 5 225 18 HOH HOH . 
N 4 HOH B 6 226 20 HOH HOH . 
N 4 HOH B 7 227 23 HOH HOH . 
N 4 HOH B 8 228 24 HOH HOH . 
N 4 HOH B 9 229 29 HOH HOH . 
N 4 HOH B 10 230 38 HOH HOH . 
N 4 HOH B 11 231 42 HOH HOH . 
N 4 HOH B 12 232 43 HOH HOH . 
N 4 HOH B 13 233 44 HOH HOH . 
O 4 HOH C 1 221 2 HOH HOH . 
O 4 HOH C 2 222 5 HOH HOH . 
O 4 HOH C 3 223 8 HOH HOH . 
O 4 HOH C 4 224 10 HOH HOH . 
O 4 HOH C 5 225 13 HOH HOH . 
O 4 HOH C 6 226 16 HOH HOH . 
O 4 HOH C 7 227 19 HOH HOH . 
O 4 HOH C 8 228 26 HOH HOH . 
O 4 HOH C 9 229 34 HOH HOH . 
O 4 HOH C 10 230 36 HOH HOH . 
O 4 HOH C 11 231 46 HOH HOH . 
P 4 HOH D 1 221 1 HOH HOH . 
P 4 HOH D 2 222 9 HOH HOH . 
P 4 HOH D 3 223 12 HOH HOH . 
P 4 HOH D 4 224 15 HOH HOH . 
P 4 HOH D 5 225 31 HOH HOH . 
P 4 HOH D 6 226 33 HOH HOH . 
P 4 HOH D 7 227 35 HOH HOH . 
P 4 HOH D 8 228 37 HOH HOH . 
P 4 HOH D 9 229 39 HOH HOH . 
P 4 HOH D 10 230 41 HOH HOH . 
P 4 HOH D 11 231 45 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 . . . L 2 25.128 49.858 130.466 1 46.48 ? N1 UMP 318 D 1 
HETATM 2 C C2 UMP . . . L 2 24.855 50.678 129.329 1 45.86 ? C2 UMP 318 D 1 
HETATM 3 N N3 UMP . . . L 2 23.739 51.389 129.355 1 45.7 ? N3 UMP 318 D 1 
HETATM 4 C C4 UMP . . . L 2 22.874 51.349 130.355 1 47.72 ? C4 UMP 318 D 1 
HETATM 5 C C5 UMP . . . L 2 23.11 50.54 131.48 1 47.69 ? C5 UMP 318 D 1 
HETATM 6 C C6 UMP . . . L 2 24.275 49.782 131.508 1 45.37 ? C6 UMP 318 D 1 
HETATM 7 O O2 UMP . . . L 2 25.647 50.778 128.327 1 42.03 ? O2 UMP 318 D 1 
HETATM 8 O O4 UMP . . . L 2 21.848 52.057 130.22 1 48.55 ? O4 UMP 318 D 1 
HETATM 9 C C1' UMP . . . L 2 26.376 49.11 130.441 1 46.08 ? C1' UMP 318 D 1 
HETATM 10 C C2' UMP . . . L 2 27.552 50.09 130.531 1 46.51 ? C2' UMP 318 D 1 
HETATM 11 C C3' UMP . . . L 2 28.459 49.514 131.591 1 47.06 ? C3' UMP 318 D 1 
HETATM 12 C C4' UMP . . . L 2 27.504 48.617 132.397 1 48.32 ? C4' UMP 318 D 1 
HETATM 13 O O3' UMP . . . L 2 29.506 48.784 130.94 1 45.74 ? O3' UMP 318 D 1 
HETATM 14 O O4' UMP . . . L 2 26.389 48.238 131.563 1 46.67 ? O4' UMP 318 D 1 
HETATM 15 C C5' UMP . . . L 2 26.969 49.287 133.662 1 48.4 ? C5' UMP 318 D 1 
HETATM 16 O O5' UMP . . . L 2 26.263 50.479 133.354 1 47.24 ? O5' UMP 318 D 1 
HETATM 17 P P UMP . . . L 2 25.518 51.287 134.517 1 49.72 ? P UMP 318 D 1 
HETATM 18 O OP1 UMP . . . L 2 25.428 52.703 133.935 1 46.58 ? OP1 UMP 318 D 1 
HETATM 19 O OP2 UMP . . . L 2 24.147 50.652 134.635 1 48.67 ? OP2 UMP 318 D 1 
HETATM 20 O OP3 UMP . . . L 2 26.353 51.074 135.756 1 45.73 ? OP3 UMP 318 D 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#