data_8OOJ
#
_model_server_result.job_id            0OPdbCMK78EUHhbhsip_-Q 
_model_server_result.datetime_utc      '2024-10-13 09:16:33' 
_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          8ooj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":302}' 
#
_entry.id    8OOJ 
#
_exptl.entry_id    8OOJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              251.239 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one 
_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            8OOJ 
_cell.length_a            137.47 
_cell.length_b            138.389 
_cell.length_c            116.825 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8OOJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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,B,E,F,G,H,M,N 1 1 
C,I,J,O 2 1,2 
D,K,L,P 3 1,3 
#
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_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 58.4125 
3 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -58.4125 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L N N 
#
_chem_comp.formula           'C11 H13 N3 O4' 
_chem_comp.formula_weight    251.239 
_chem_comp.id                VVC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one 
_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
C10 C11 VVC sing 416 n n 
C10 C5 VVC sing 417 n n 
C11 O4 VVC sing 418 n n 
C11 C3 VVC sing 419 n n 
O3 C9 VVC doub 420 n n 
O1 C4 VVC sing 421 n n 
C9 N1 VVC sing 422 n n 
C9 N3 VVC sing 423 n n 
N1 C5 VVC sing 424 n n 
N1 C6 VVC sing 425 n n 
N3 C8 VVC doub 426 n n 
C5 O2 VVC sing 427 n n 
C8 N2 VVC sing 428 n n 
C8 C7 VVC sing 429 n n 
C6 C7 VVC doub 430 n n 
C3 C4 VVC sing 431 n n 
C3 O2 VVC sing 432 n n 
C3 C2 VVC sing 433 n n 
C2 C1 VVC trip 434 n n 
C4 H1 VVC sing 435 n n 
C4 H2 VVC sing 436 n n 
C5 H3 VVC sing 437 n n 
C6 H4 VVC sing 438 n n 
C11 H5 VVC sing 439 n n 
C7 H6 VVC sing 440 n n 
C10 H7 VVC sing 441 n n 
C10 H8 VVC sing 442 n n 
N2 H9 VVC sing 443 n n 
N2 H10 VVC sing 444 n n 
C1 H11 VVC sing 445 n n 
O1 H12 VVC sing 446 n n 
O4 H13 VVC sing 447 n n 
#
_atom_sites.entry_id                     8OOJ 
_atom_sites.fract_transf_matrix[1][1]    0.007274 
_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]    0.007226 
_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]    0.00856 
_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 UDP A 1 301 301 UDP UDP . 
F 3 VVC A 1 302 302 VVC DRG . 
G 2 UDP B 1 301 301 UDP UDP . 
H 3 VVC B 1 302 302 VVC DRG . 
I 2 UDP C 1 301 301 UDP UDP . 
J 3 VVC C 1 302 302 VVC DRG . 
K 2 UDP D 1 301 301 UDP UDP . 
L 3 VVC D 1 302 302 VVC DRG . 
M 4 HOH A 1 401 41 HOH HOH . 
M 4 HOH A 2 402 48 HOH HOH . 
M 4 HOH A 3 403 24 HOH HOH . 
M 4 HOH A 4 404 10 HOH HOH . 
M 4 HOH A 5 405 42 HOH HOH . 
M 4 HOH A 6 406 38 HOH HOH . 
N 4 HOH B 1 401 43 HOH HOH . 
N 4 HOH B 2 402 52 HOH HOH . 
N 4 HOH B 3 403 49 HOH HOH . 
N 4 HOH B 4 404 3 HOH HOH . 
N 4 HOH B 5 405 9 HOH HOH . 
N 4 HOH B 6 406 17 HOH HOH . 
N 4 HOH B 7 407 18 HOH HOH . 
N 4 HOH B 8 408 39 HOH HOH . 
N 4 HOH B 9 409 37 HOH HOH . 
N 4 HOH B 10 410 2 HOH HOH . 
N 4 HOH B 11 411 20 HOH HOH . 
N 4 HOH B 12 412 5 HOH HOH . 
N 4 HOH B 13 413 50 HOH HOH . 
N 4 HOH B 14 414 53 HOH HOH . 
N 4 HOH B 15 415 12 HOH HOH . 
N 4 HOH B 16 416 47 HOH HOH . 
N 4 HOH B 17 417 29 HOH HOH . 
N 4 HOH B 18 418 22 HOH HOH . 
N 4 HOH B 19 419 26 HOH HOH . 
O 4 HOH C 1 401 23 HOH HOH . 
O 4 HOH C 2 402 33 HOH HOH . 
O 4 HOH C 3 403 35 HOH HOH . 
O 4 HOH C 4 404 25 HOH HOH . 
O 4 HOH C 5 405 30 HOH HOH . 
O 4 HOH C 6 406 46 HOH HOH . 
O 4 HOH C 7 407 51 HOH HOH . 
O 4 HOH C 8 408 8 HOH HOH . 
O 4 HOH C 9 409 21 HOH HOH . 
O 4 HOH C 10 410 40 HOH HOH . 
O 4 HOH C 11 411 1 HOH HOH . 
O 4 HOH C 12 412 13 HOH HOH . 
O 4 HOH C 13 413 16 HOH HOH . 
O 4 HOH C 14 414 34 HOH HOH . 
O 4 HOH C 15 415 36 HOH HOH . 
P 4 HOH D 1 401 44 HOH HOH . 
P 4 HOH D 2 402 27 HOH HOH . 
P 4 HOH D 3 403 28 HOH HOH . 
P 4 HOH D 4 404 14 HOH HOH . 
P 4 HOH D 5 405 6 HOH HOH . 
P 4 HOH D 6 406 7 HOH HOH . 
P 4 HOH D 7 407 19 HOH HOH . 
P 4 HOH D 8 408 32 HOH HOH . 
P 4 HOH D 9 409 45 HOH HOH . 
P 4 HOH D 10 410 11 HOH HOH . 
P 4 HOH D 11 411 4 HOH HOH . 
P 4 HOH D 12 412 15 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 C C4 VVC . . . L 3 16.89 -10.262 -21.118 1 47.06 ? C4 VVC 302 D 1 
HETATM 2 C C5 VVC . . . L 3 14.04 -8.639 -20.143 1 41.29 ? C5 VVC 302 D 1 
HETATM 3 C C6 VVC . . . L 3 12.972 -10.866 -20.086 1 40.34 ? C6 VVC 302 D 1 
HETATM 4 C C11 VVC . . . L 3 16.312 -8.362 -19.544 1 42.66 ? C11 VVC 302 D 1 
HETATM 5 C C7 VVC . . . L 3 11.893 -11.664 -20.064 1 38.82 ? C7 VVC 302 D 1 
HETATM 6 C C8 VVC . . . L 3 10.612 -11.044 -20.043 1 38.49 ? C8 VVC 302 D 1 
HETATM 7 C C9 VVC . . . L 3 11.579 -8.917 -20.072 1 37.82 ? C9 VVC 302 D 1 
HETATM 8 C C10 VVC . . . L 3 14.961 -8.699 -18.923 1 42.38 ? C10 VVC 302 D 1 
HETATM 9 N N1 VVC . . . L 3 12.846 -9.51 -20.085 1 40.66 ? N1 VVC 302 D 1 
HETATM 10 N N2 VVC . . . L 3 9.504 -11.775 -20.021 1 40.01 ? N2 VVC 302 D 1 
HETATM 11 C C3 VVC . . . L 3 16.207 -8.909 -20.982 1 43.6 ? C3 VVC 302 D 1 
HETATM 12 N N3 VVC . . . L 3 10.482 -9.71 -20.049 1 34.26 ? N3 VVC 302 D 1 
HETATM 13 C C1 VVC . . . L 3 17.181 -7.145 -22.703 1 48.26 ? C1 VVC 302 D 1 
HETATM 14 C C2 VVC . . . L 3 16.765 -7.939 -21.941 1 46.02 ? C2 VVC 302 D 1 
HETATM 15 O O1 VVC . . . L 3 16.714 -11.037 -19.937 1 49.69 ? O1 VVC 302 D 1 
HETATM 16 O O2 VVC . . . L 3 14.822 -9.082 -21.236 1 41.89 ? O2 VVC 302 D 1 
HETATM 17 O O3 VVC . . . L 3 11.492 -7.686 -20.086 1 40.02 ? O3 VVC 302 D 1 
HETATM 18 O O4 VVC . . . L 3 16.607 -6.972 -19.515 1 43.39 ? O4 VVC 302 D 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           18 
#