data_7K1O
#
_model_server_result.job_id            1dxIzp0R8xdzYkI-ycTLXQ 
_model_server_result.datetime_utc      '2024-11-08 15:56:26' 
_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          7k1o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    7K1O 
#
_exptl.entry_id    7K1O 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            7K1O 
_cell.length_a            87.46 
_cell.length_b            151.321 
_cell.length_c            197.518 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7K1O 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    'C 2c 2' 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 3_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 87.46 0 -98.759 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 D N N 
? 2 F N N 
? 2 H N N 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                VQV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
O3P P VQV doub 385 n n 
P O1P VQV sing 386 n n 
P O5' VQV sing 387 n n 
P O2P VQV sing 388 n n 
O5' C5' VQV sing 389 n n 
C5' C4' VQV sing 390 n n 
O4' C4' VQV sing 391 n n 
O4' C1' VQV sing 392 n n 
C4' C3' VQV sing 393 n n 
C6 C5 VQV doub 394 n n 
C6 N1 VQV sing 395 n n 
C5 C4 VQV sing 396 n n 
C1' N1 VQV sing 397 n n 
C1' C2' VQV sing 398 n n 
N1 C2 VQV sing 399 n n 
O2B P2 VQV doub 400 n n 
C4 O4 VQV doub 401 n n 
C4 N3 VQV sing 402 n n 
C3' O3' VQV sing 403 n n 
C3' C2' VQV sing 404 n n 
O3' P2 VQV sing 405 n n 
C2' O2' VQV sing 406 n n 
C2 N3 VQV sing 407 n n 
C2 O2 VQV doub 408 n n 
P2 O2C VQV sing 409 n n 
P2 O2A VQV sing 410 n n 
C6 H1 VQV sing 411 n n 
C5 H2 VQV sing 412 n n 
C1' H3 VQV sing 413 n n 
C2' H4 VQV sing 414 n n 
C3' H5 VQV sing 415 n n 
C4' H6 VQV sing 416 n n 
C5' H7 VQV sing 417 n n 
C5' H8 VQV sing 418 n n 
N3 H9 VQV sing 419 n n 
O1P H10 VQV sing 420 n n 
O2' H11 VQV sing 421 n n 
O2A H12 VQV sing 422 n n 
O2C H13 VQV sing 423 n n 
O2P H14 VQV sing 424 n n 
#
_atom_sites.entry_id                     7K1O 
_atom_sites.fract_transf_matrix[1][1]    0.011434 
_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]    0.006608 
_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]    0.005063 
_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
D 2 VQV A 1 401 401 VQV U53 . 
E 3 EDO A 1 402 501 EDO EDO . 
F 2 VQV B 1 401 401 VQV U53 . 
G 3 EDO B 1 402 501 EDO EDO . 
H 2 VQV C 1 401 401 VQV U53 . 
I 3 EDO C 1 402 501 EDO EDO . 
J 4 HOH A 1 501 20 HOH HOH . 
J 4 HOH A 2 502 16 HOH HOH . 
J 4 HOH A 3 503 17 HOH HOH . 
J 4 HOH A 4 504 12 HOH HOH . 
J 4 HOH A 5 505 2 HOH HOH . 
J 4 HOH A 6 506 8 HOH HOH . 
J 4 HOH A 7 507 31 HOH HOH . 
J 4 HOH A 8 508 9 HOH HOH . 
J 4 HOH A 9 509 38 HOH HOH . 
J 4 HOH A 10 510 35 HOH HOH . 
J 4 HOH A 11 511 52 HOH HOH . 
J 4 HOH A 12 512 29 HOH HOH . 
J 4 HOH A 13 513 53 HOH HOH . 
J 4 HOH A 14 514 40 HOH HOH . 
J 4 HOH A 15 515 24 HOH HOH . 
J 4 HOH A 16 516 18 HOH HOH . 
J 4 HOH A 17 517 7 HOH HOH . 
J 4 HOH A 18 518 34 HOH HOH . 
J 4 HOH A 19 519 6 HOH HOH . 
J 4 HOH A 20 520 54 HOH HOH . 
J 4 HOH A 21 521 41 HOH HOH . 
K 4 HOH B 1 501 14 HOH HOH . 
K 4 HOH B 2 502 45 HOH HOH . 
K 4 HOH B 3 503 32 HOH HOH . 
K 4 HOH B 4 504 47 HOH HOH . 
K 4 HOH B 5 505 43 HOH HOH . 
K 4 HOH B 6 506 37 HOH HOH . 
K 4 HOH B 7 507 30 HOH HOH . 
K 4 HOH B 8 508 26 HOH HOH . 
K 4 HOH B 9 509 36 HOH HOH . 
K 4 HOH B 10 510 39 HOH HOH . 
K 4 HOH B 11 511 19 HOH HOH . 
L 4 HOH C 1 501 46 HOH HOH . 
L 4 HOH C 2 502 21 HOH HOH . 
L 4 HOH C 3 503 50 HOH HOH . 
L 4 HOH C 4 504 5 HOH HOH . 
L 4 HOH C 5 505 10 HOH HOH . 
L 4 HOH C 6 506 44 HOH HOH . 
L 4 HOH C 7 507 51 HOH HOH . 
L 4 HOH C 8 508 4 HOH HOH . 
L 4 HOH C 9 509 49 HOH HOH . 
L 4 HOH C 10 510 48 HOH HOH . 
L 4 HOH C 11 511 25 HOH HOH . 
L 4 HOH C 12 512 33 HOH HOH . 
L 4 HOH C 13 513 27 HOH HOH . 
L 4 HOH C 14 514 22 HOH HOH . 
L 4 HOH C 15 515 42 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 O O2 VQV . . . F 2 16.464 52.669 -86.775 0.95 103.8 ? O2 VQV 401 B 1 
HETATM 2 N N1 VQV . . . F 2 16.671 53.505 -84.707 0.95 106.19 ? N1 VQV 401 B 1 
HETATM 3 C C4 VQV . . . F 2 15.104 55.601 -85.498 0.95 111.21 ? C4 VQV 401 B 1 
HETATM 4 C C2 VQV . . . F 2 16.191 53.576 -85.96 0.95 107.27 ? C2 VQV 401 B 1 
HETATM 5 C C6 VQV . . . F 2 16.386 54.471 -83.82 0.95 104.79 ? C6 VQV 401 B 1 
HETATM 6 C C5 VQV . . . F 2 15.59 55.548 -84.197 0.95 107.43 ? C5 VQV 401 B 1 
HETATM 7 C C1' VQV . . . F 2 17.517 52.359 -84.328 0.95 101.01 ? C1' VQV 401 B 1 
HETATM 8 C C2' VQV . . . F 2 18.978 52.581 -84.736 0.95 96.33 ? C2' VQV 401 B 1 
HETATM 9 C C3' VQV . . . F 2 19.796 52.263 -83.502 0.95 91.99 ? C3' VQV 401 B 1 
HETATM 10 C C4' VQV . . . F 2 18.8 52.371 -82.357 0.95 94.86 ? C4' VQV 401 B 1 
HETATM 11 C C5' VQV . . . F 2 19.088 51.389 -81.228 0.95 90.27 ? C5' VQV 401 B 1 
HETATM 12 N N3 VQV . . . F 2 15.414 54.61 -86.36 0.95 110.27 ? N3 VQV 401 B 1 
HETATM 13 O O1P VQV . . . F 2 17.898 53.173 -79.167 0.95 98.65 ? O1P VQV 401 B 1 
HETATM 14 O O2' VQV . . . F 2 19.216 53.955 -85.071 0.95 99.26 ? O2' VQV 401 B 1 
HETATM 15 O O2A VQV . . . F 2 22.62 49.882 -83.539 0.95 77.79 ? O2A VQV 401 B 1 
HETATM 16 O O2B VQV . . . F 2 21.281 49.74 -85.613 0.95 79.4 ? O2B VQV 401 B 1 
HETATM 17 O O2C VQV . . . F 2 22.304 51.887 -84.934 0.95 80.69 ? O2C VQV 401 B 1 
HETATM 18 O O2P VQV . . . F 2 20.11 53.348 -78.084 0.95 96.43 ? O2P VQV 401 B 1 
HETATM 19 O O3' VQV . . . F 2 20.325 50.944 -83.596 0.95 86.56 ? O3' VQV 401 B 1 
HETATM 20 O O3P VQV . . . F 2 19.682 54.569 -80.185 0.95 96.45 ? O3P VQV 401 B 1 
HETATM 21 O O4 VQV . . . F 2 14.321 56.64 -85.907 0.95 111.46 ? O4 VQV 401 B 1 
HETATM 22 O O4' VQV . . . F 2 17.502 52.134 -82.914 0.95 98.3 ? O4' VQV 401 B 1 
HETATM 23 O O5' VQV . . . F 2 19.902 52.019 -80.237 0.95 89.49 ? O5' VQV 401 B 1 
HETATM 24 P P VQV . . . F 2 19.384 53.306 -79.409 0.95 96.95 ? P VQV 401 B 1 
HETATM 25 P P2 VQV . . . F 2 21.658 50.614 -84.445 0.95 79.51 ? P2 VQV 401 B 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           251 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           25 
#