data_5X5Q
#
_model_server_result.job_id            MfuWEluuu3GrDgo3mtVfHQ 
_model_server_result.datetime_utc      '2025-07-27 20:03:16' 
_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          5x5q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":401}' 
#
_entry.id    5X5Q 
#
_exptl.entry_id    5X5Q 
_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    6 
_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            5X5Q 
_cell.length_a            107.835 
_cell.length_b            107.835 
_cell.length_c            314.951 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5X5Q 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
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 
PISA dimeric 2 author_and_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,D,G,H,M,N,S,V 1 1 
B,E,I,J,O,P,T 2 1 
C,F,K,L,Q,R,U,W 3 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 G N N 
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q 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                     5X5Q 
_atom_sites.fract_transf_matrix[1][1]    0.009273 
_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]    0.009273 
_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]    0.003175 
_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
G 2 UMP A 1 401 1 UMP UMP . 
H 3 D16 A 1 402 1 D16 RTX . 
I 2 UMP B 1 401 2 UMP UMP . 
J 3 D16 B 1 402 2 D16 RTX . 
K 2 UMP C 1 401 3 UMP UMP . 
L 3 D16 C 1 402 3 D16 RTX . 
M 2 UMP D 1 401 4 UMP UMP . 
N 3 D16 D 1 402 4 D16 RTX . 
O 2 UMP E 1 401 5 UMP UMP . 
P 3 D16 E 1 402 5 D16 RTX . 
Q 2 UMP F 1 401 6 UMP UMP . 
R 3 D16 F 1 402 6 D16 RTX . 
S 4 HOH A 1 501 1 HOH HOH . 
S 4 HOH A 2 502 9 HOH HOH . 
T 4 HOH B 1 501 5 HOH HOH . 
T 4 HOH B 2 502 8 HOH HOH . 
T 4 HOH B 3 503 2 HOH HOH . 
T 4 HOH B 4 504 4 HOH HOH . 
U 4 HOH C 1 501 3 HOH HOH . 
V 4 HOH D 1 501 7 HOH HOH . 
V 4 HOH D 2 502 10 HOH HOH . 
W 4 HOH F 1 501 6 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 . . . M 2 16.782 15.426 23.798 1 35.08 ? N1 UMP 401 D 1 
HETATM 2 C C2 UMP . . . M 2 16.482 16.502 22.888 1 34.31 ? C2 UMP 401 D 1 
HETATM 3 N N3 UMP . . . M 2 15.763 17.612 23.452 1 32.55 ? N3 UMP 401 D 1 
HETATM 4 C C4 UMP . . . M 2 15.356 17.707 24.795 1 33.16 ? C4 UMP 401 D 1 
HETATM 5 C C5 UMP . . . M 2 15.679 16.637 25.711 1 33.04 ? C5 UMP 401 D 1 
HETATM 6 C C6 UMP . . . M 2 16.399 15.494 25.193 1 34.6 ? C6 UMP 401 D 1 
HETATM 7 O O2 UMP . . . M 2 16.771 16.505 21.712 1 33.76 ? O2 UMP 401 D 1 
HETATM 8 O O4 UMP . . . M 2 14.748 18.681 25.193 1 38.11 ? O4 UMP 401 D 1 
HETATM 9 C C1' UMP . . . M 2 17.498 14.247 23.383 1 35.73 ? C1' UMP 401 D 1 
HETATM 10 C C2' UMP . . . M 2 18.804 14.028 22.752 1 37.24 ? C2' UMP 401 D 1 
HETATM 11 C C3' UMP . . . M 2 19.191 12.673 23.076 1 37.61 ? C3' UMP 401 D 1 
HETATM 12 C C4' UMP . . . M 2 18.461 12.39 24.32 1 37.05 ? C4' UMP 401 D 1 
HETATM 13 O O3' UMP . . . M 2 18.751 11.761 22.104 1 37.3 ? O3' UMP 401 D 1 
HETATM 14 O O4' UMP . . . M 2 17.248 13.127 24.21 1 37.57 ? O4' UMP 401 D 1 
HETATM 15 C C5' UMP . . . M 2 19.336 12.749 25.453 1 36.97 ? C5' UMP 401 D 1 
HETATM 16 O O5' UMP . . . M 2 20.385 11.88 25.615 1 37.44 ? O5' UMP 401 D 1 
HETATM 17 P P UMP . . . M 2 21.641 12.337 26.41 1 40.06 ? P UMP 401 D 1 
HETATM 18 O OP1 UMP . . . M 2 21.172 12.99 27.692 1 35.14 -1 OP1 UMP 401 D 1 
HETATM 19 O OP2 UMP . . . M 2 22.605 11.183 26.688 1 37.86 ? OP2 UMP 401 D 1 
HETATM 20 O OP3 UMP . . . M 2 22.37 13.304 25.438 1 35.6 -1 OP3 UMP 401 D 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    61 
_model_server_stats.query_time_ms           452 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#