data_5X69
#
_model_server_result.job_id            Gm8fOxjz-epGkvhy3Oze-w 
_model_server_result.datetime_utc      '2024-11-22 23:05:14' 
_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          5x69 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":401}' 
#
_entry.id    5X69 
#
_exptl.entry_id    5X69 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          3 
_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            5X69 
_cell.length_a            109.353 
_cell.length_b            109.353 
_cell.length_c            315.38 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5X69 
_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,J,M,P 1 1 
B,E,I,K,N,Q 2 1 
C,F,L,O,R 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
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 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 390 n n 
N1 C6 UMP sing 391 n n 
N1 C1' UMP sing 392 n n 
C2 N3 UMP sing 393 n n 
C2 O2 UMP doub 394 n n 
N3 C4 UMP sing 395 n n 
N3 HN3 UMP sing 396 n n 
C4 C5 UMP sing 397 n n 
C4 O4 UMP doub 398 n n 
C5 C6 UMP doub 399 n n 
C5 H5 UMP sing 400 n n 
C6 H6 UMP sing 401 n n 
C1' C2' UMP sing 402 n n 
C1' O4' UMP sing 403 n n 
C1' H1' UMP sing 404 n n 
C2' C3' UMP sing 405 n n 
C2' H2' UMP sing 406 n n 
C2' "H2''" UMP sing 407 n n 
C3' C4' UMP sing 408 n n 
C3' O3' UMP sing 409 n n 
C3' H3' UMP sing 410 n n 
C4' O4' UMP sing 411 n n 
C4' C5' UMP sing 412 n n 
C4' H4' UMP sing 413 n n 
O3' HO3' UMP sing 414 n n 
C5' O5' UMP sing 415 n n 
C5' H5' UMP sing 416 n n 
C5' "H5''" UMP sing 417 n n 
O5' P UMP sing 418 n n 
P OP1 UMP doub 419 n n 
P OP2 UMP sing 420 n n 
P OP3 UMP sing 421 n n 
OP2 HOP2 UMP sing 422 n n 
OP3 HOP3 UMP sing 423 n n 
#
_atom_sites.entry_id                     5X69 
_atom_sites.fract_transf_matrix[1][1]    0.009145 
_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]    0.009145 
_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]    0.003171 
_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 7ZC A 1 401 1 7ZC 1E3 . 
H 3 UMP A 1 402 1 UMP UMP . 
I 3 UMP B 1 401 2 UMP UMP . 
J 3 UMP D 1 401 3 UMP UMP . 
K 2 7ZC E 1 401 2 7ZC 1E3 . 
L 3 UMP F 1 401 4 UMP UMP . 
M 4 HOH A 1 501 38 HOH HOH . 
M 4 HOH A 2 502 46 HOH HOH . 
M 4 HOH A 3 503 50 HOH HOH . 
M 4 HOH A 4 504 20 HOH HOH . 
M 4 HOH A 5 505 33 HOH HOH . 
M 4 HOH A 6 506 23 HOH HOH . 
M 4 HOH A 7 507 35 HOH HOH . 
M 4 HOH A 8 508 11 HOH HOH . 
M 4 HOH A 9 509 18 HOH HOH . 
M 4 HOH A 10 510 44 HOH HOH . 
M 4 HOH A 11 511 1 HOH HOH . 
M 4 HOH A 12 512 16 HOH HOH . 
M 4 HOH A 13 513 42 HOH HOH . 
M 4 HOH A 14 514 41 HOH HOH . 
M 4 HOH A 15 515 75 HOH HOH . 
M 4 HOH A 16 516 76 HOH HOH . 
M 4 HOH A 17 517 77 HOH HOH . 
N 4 HOH B 1 501 58 HOH HOH . 
N 4 HOH B 2 502 28 HOH HOH . 
N 4 HOH B 3 503 22 HOH HOH . 
N 4 HOH B 4 504 32 HOH HOH . 
N 4 HOH B 5 505 9 HOH HOH . 
N 4 HOH B 6 506 65 HOH HOH . 
N 4 HOH B 7 507 49 HOH HOH . 
N 4 HOH B 8 508 6 HOH HOH . 
N 4 HOH B 9 509 74 HOH HOH . 
N 4 HOH B 10 510 47 HOH HOH . 
N 4 HOH B 11 511 24 HOH HOH . 
N 4 HOH B 12 512 37 HOH HOH . 
N 4 HOH B 13 513 64 HOH HOH . 
N 4 HOH B 14 514 40 HOH HOH . 
N 4 HOH B 15 515 3 HOH HOH . 
O 4 HOH C 1 401 63 HOH HOH . 
O 4 HOH C 2 402 29 HOH HOH . 
O 4 HOH C 3 403 34 HOH HOH . 
O 4 HOH C 4 404 51 HOH HOH . 
O 4 HOH C 5 405 2 HOH HOH . 
O 4 HOH C 6 406 8 HOH HOH . 
O 4 HOH C 7 407 55 HOH HOH . 
O 4 HOH C 8 408 39 HOH HOH . 
O 4 HOH C 9 409 73 HOH HOH . 
P 4 HOH D 1 501 10 HOH HOH . 
P 4 HOH D 2 502 17 HOH HOH . 
P 4 HOH D 3 503 13 HOH HOH . 
P 4 HOH D 4 504 36 HOH HOH . 
P 4 HOH D 5 505 66 HOH HOH . 
P 4 HOH D 6 506 25 HOH HOH . 
P 4 HOH D 7 507 30 HOH HOH . 
P 4 HOH D 8 508 45 HOH HOH . 
P 4 HOH D 9 509 67 HOH HOH . 
P 4 HOH D 10 510 78 HOH HOH . 
P 4 HOH D 11 511 79 HOH HOH . 
Q 4 HOH E 1 501 52 HOH HOH . 
Q 4 HOH E 2 502 5 HOH HOH . 
Q 4 HOH E 3 503 12 HOH HOH . 
Q 4 HOH E 4 504 14 HOH HOH . 
Q 4 HOH E 5 505 43 HOH HOH . 
Q 4 HOH E 6 506 48 HOH HOH . 
Q 4 HOH E 7 507 31 HOH HOH . 
Q 4 HOH E 8 508 56 HOH HOH . 
Q 4 HOH E 9 509 57 HOH HOH . 
Q 4 HOH E 10 510 15 HOH HOH . 
Q 4 HOH E 11 511 53 HOH HOH . 
Q 4 HOH E 12 512 4 HOH HOH . 
Q 4 HOH E 13 513 26 HOH HOH . 
Q 4 HOH E 14 514 61 HOH HOH . 
Q 4 HOH E 15 515 60 HOH HOH . 
Q 4 HOH E 16 516 70 HOH HOH . 
Q 4 HOH E 17 517 72 HOH HOH . 
Q 4 HOH E 18 518 71 HOH HOH . 
Q 4 HOH E 19 519 69 HOH HOH . 
R 4 HOH F 1 501 19 HOH HOH . 
R 4 HOH F 2 502 21 HOH HOH . 
R 4 HOH F 3 503 59 HOH HOH . 
R 4 HOH F 4 504 7 HOH HOH . 
R 4 HOH F 5 505 27 HOH HOH . 
R 4 HOH F 6 506 54 HOH HOH . 
R 4 HOH F 7 507 62 HOH HOH . 
R 4 HOH F 8 508 68 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 3 -38.772 37.18 -54.894 1 80.88 ? N1 UMP 401 D 1 
HETATM 2 C C2 UMP . . . J 3 -37.731 37.645 -55.853 1 79.39 ? C2 UMP 401 D 1 
HETATM 3 N N3 UMP . . . J 3 -36.664 38.49 -55.306 1 80.69 ? N3 UMP 401 D 1 
HETATM 4 C C4 UMP . . . J 3 -36.542 38.88 -53.933 1 79.52 ? C4 UMP 401 D 1 
HETATM 5 C C5 UMP . . . J 3 -37.573 38.413 -52.977 1 81.97 ? C5 UMP 401 D 1 
HETATM 6 C C6 UMP . . . J 3 -38.683 37.565 -53.47 1 82.38 ? C6 UMP 401 D 1 
HETATM 7 O O2 UMP . . . J 3 -37.692 37.395 -57.046 1 71.57 ? O2 UMP 401 D 1 
HETATM 8 O O4 UMP . . . J 3 -35.612 39.584 -53.571 1 75.18 ? O4 UMP 401 D 1 
HETATM 9 C C1' UMP . . . J 3 -39.918 36.306 -55.275 1 76.96 ? C1' UMP 401 D 1 
HETATM 10 C C2' UMP . . . J 3 -40.081 34.979 -55.912 1 75.8 ? C2' UMP 401 D 1 
HETATM 11 C C3' UMP . . . J 3 -41.466 34.597 -55.759 1 70.88 ? C3' UMP 401 D 1 
HETATM 12 C C4' UMP . . . J 3 -41.861 35.245 -54.525 1 68.36 ? C4' UMP 401 D 1 
HETATM 13 O O3' UMP . . . J 3 -42.292 35.12 -56.762 1 70.31 ? O3' UMP 401 D 1 
HETATM 14 O O4' UMP . . . J 3 -41.093 36.425 -54.482 1 77.25 ? O4' UMP 401 D 1 
HETATM 15 C C5' UMP . . . J 3 -41.561 34.358 -53.392 1 66.39 ? C5' UMP 401 D 1 
HETATM 16 O O5' UMP . . . J 3 -42.327 33.225 -53.362 1 64.34 ? O5' UMP 401 D 1 
HETATM 17 P P UMP . . . J 3 -41.823 31.987 -52.582 1 67.58 ? P UMP 401 D 1 
HETATM 18 O OP1 UMP . . . J 3 -41.288 32.399 -51.222 1 67.69 ? OP1 UMP 401 D 1 
HETATM 19 O OP2 UMP . . . J 3 -42.872 30.895 -52.452 1 72.36 -1 OP2 UMP 401 D 1 
HETATM 20 O OP3 UMP . . . J 3 -40.688 31.498 -53.429 1 69.32 -1 OP3 UMP 401 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#