data_2NO9
#
_model_server_result.job_id            4YDK2Nq10fmzG6YIrqJcGQ 
_model_server_result.datetime_utc      '2024-12-24 03:42:49' 
_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          2no9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    2NO9 
#
_exptl.entry_id    2NO9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              213.191 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-AMINO-1-[(2S,4S)-2-(HYDROXYMETHYL)-1,3-DIOXOLAN-4-YL]PYRIMIDIN-2(1H)-ONE 
_entity.pdbx_number_of_molecules    2 
_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            2NO9 
_cell.length_a            52.85 
_cell.length_b            134.46 
_cell.length_c            155.34 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2NO9 
_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 tetrameric 4 software_defined_assembly 2 
PISA tetrameric 4 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,C,D,E,F,G,H 1 1 
A,C,D,G 2 1,2 
B,E,F,H 2 3,4 
A,B,C,D,E,F,G,H 3 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' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 134.46 155.34 
3 'crystal symmetry operation' 5_545 x+1/2,y-1/2,z 1 0 0 0 1 0 0 0 1 26.425 -67.23 0 
4 'crystal symmetry operation' 8_566 x+1/2,-y+3/2,-z+1 1 0 0 0 -1 0 0 0 -1 26.425 201.69 155.34 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C8 H11 N3 O4' 
_chem_comp.formula_weight    213.191 
_chem_comp.id                LTT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-AMINO-1-[(2S,4S)-2-(HYDROXYMETHYL)-1,3-DIOXOLAN-4-YL]PYRIMIDIN-2(1H)-ONE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "(-)-L-2',3'-DIDEOXY-3'-OXACYTIDINE;TROXACITABINE;TROXATYL" 
#
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
O1 C1 LTT doub 238 n n 
C1 N2 LTT sing 239 n y 
C1 N1 LTT sing 240 n y 
N2 C3 LTT doub 241 n y 
C3 N3 LTT sing 242 n n 
C3 C5 LTT sing 243 n y 
N3 HN31 LTT sing 244 n n 
N3 HN32 LTT sing 245 n n 
C5 C7 LTT doub 246 n y 
C5 H5 LTT sing 247 n n 
C7 N1 LTT sing 248 n y 
C7 H7 LTT sing 249 n n 
N1 C4 LTT sing 250 n n 
C4 O3 LTT sing 251 n n 
C4 C6 LTT sing 252 n n 
C4 H4 LTT sing 253 n n 
O3 C2 LTT sing 254 n n 
C2 C8 LTT sing 255 n n 
C2 O2 LTT sing 256 n n 
C2 H2 LTT sing 257 n n 
C8 O4 LTT sing 258 n n 
C8 H81 LTT sing 259 n n 
C8 H82 LTT sing 260 n n 
O4 HO4 LTT sing 261 n n 
O2 C6 LTT sing 262 n n 
C6 H61 LTT sing 263 n n 
C6 H62 LTT sing 264 n n 
#
_atom_sites.entry_id                     2NO9 
_atom_sites.fract_transf_matrix[1][1]    0.018921 
_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]    0.007437 
_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]    0.006437 
_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
C 2 ADP A 1 301 301 ADP ADP . 
D 3 LTT A 1 302 1 LTT TRO . 
E 2 ADP B 1 301 301 ADP ADP . 
F 3 LTT B 1 302 2 LTT TRO . 
G 4 HOH A 1 303 1 HOH HOH . 
G 4 HOH A 2 304 2 HOH HOH . 
G 4 HOH A 3 305 3 HOH HOH . 
G 4 HOH A 4 306 4 HOH HOH . 
G 4 HOH A 5 307 5 HOH HOH . 
G 4 HOH A 6 308 7 HOH HOH . 
G 4 HOH A 7 309 8 HOH HOH . 
G 4 HOH A 8 310 9 HOH HOH . 
G 4 HOH A 9 311 10 HOH HOH . 
G 4 HOH A 10 312 11 HOH HOH . 
G 4 HOH A 11 313 12 HOH HOH . 
G 4 HOH A 12 314 16 HOH HOH . 
G 4 HOH A 13 315 17 HOH HOH . 
G 4 HOH A 14 316 18 HOH HOH . 
G 4 HOH A 15 317 20 HOH HOH . 
G 4 HOH A 16 318 24 HOH HOH . 
G 4 HOH A 17 319 26 HOH HOH . 
G 4 HOH A 18 320 28 HOH HOH . 
G 4 HOH A 19 321 29 HOH HOH . 
G 4 HOH A 20 322 31 HOH HOH . 
G 4 HOH A 21 323 32 HOH HOH . 
G 4 HOH A 22 324 33 HOH HOH . 
G 4 HOH A 23 325 35 HOH HOH . 
G 4 HOH A 24 326 36 HOH HOH . 
G 4 HOH A 25 327 40 HOH HOH . 
G 4 HOH A 26 328 41 HOH HOH . 
G 4 HOH A 27 329 42 HOH HOH . 
G 4 HOH A 28 330 46 HOH HOH . 
G 4 HOH A 29 331 48 HOH HOH . 
G 4 HOH A 30 332 49 HOH HOH . 
G 4 HOH A 31 333 50 HOH HOH . 
G 4 HOH A 32 334 51 HOH HOH . 
G 4 HOH A 33 335 55 HOH HOH . 
G 4 HOH A 34 336 56 HOH HOH . 
G 4 HOH A 35 337 57 HOH HOH . 
G 4 HOH A 36 338 58 HOH HOH . 
G 4 HOH A 37 339 62 HOH HOH . 
G 4 HOH A 38 340 63 HOH HOH . 
G 4 HOH A 39 341 66 HOH HOH . 
G 4 HOH A 40 342 68 HOH HOH . 
G 4 HOH A 41 343 69 HOH HOH . 
G 4 HOH A 42 344 70 HOH HOH . 
G 4 HOH A 43 345 71 HOH HOH . 
G 4 HOH A 44 346 72 HOH HOH . 
G 4 HOH A 45 347 73 HOH HOH . 
G 4 HOH A 46 348 74 HOH HOH . 
G 4 HOH A 47 349 78 HOH HOH . 
G 4 HOH A 48 350 81 HOH HOH . 
G 4 HOH A 49 351 82 HOH HOH . 
H 4 HOH B 1 303 6 HOH HOH . 
H 4 HOH B 2 304 13 HOH HOH . 
H 4 HOH B 3 305 14 HOH HOH . 
H 4 HOH B 4 306 15 HOH HOH . 
H 4 HOH B 5 307 19 HOH HOH . 
H 4 HOH B 6 308 21 HOH HOH . 
H 4 HOH B 7 309 22 HOH HOH . 
H 4 HOH B 8 310 23 HOH HOH . 
H 4 HOH B 9 311 25 HOH HOH . 
H 4 HOH B 10 312 27 HOH HOH . 
H 4 HOH B 11 313 30 HOH HOH . 
H 4 HOH B 12 314 34 HOH HOH . 
H 4 HOH B 13 315 37 HOH HOH . 
H 4 HOH B 14 316 38 HOH HOH . 
H 4 HOH B 15 317 39 HOH HOH . 
H 4 HOH B 16 318 43 HOH HOH . 
H 4 HOH B 17 319 44 HOH HOH . 
H 4 HOH B 18 320 45 HOH HOH . 
H 4 HOH B 19 321 47 HOH HOH . 
H 4 HOH B 20 322 52 HOH HOH . 
H 4 HOH B 21 323 53 HOH HOH . 
H 4 HOH B 22 324 54 HOH HOH . 
H 4 HOH B 23 325 59 HOH HOH . 
H 4 HOH B 24 326 61 HOH HOH . 
H 4 HOH B 25 327 64 HOH HOH . 
H 4 HOH B 26 328 67 HOH HOH . 
H 4 HOH B 27 329 75 HOH HOH . 
H 4 HOH B 28 330 77 HOH HOH . 
H 4 HOH B 29 331 79 HOH HOH . 
H 4 HOH B 30 332 80 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 O1 LTT . . . F 3 38.761 93.941 92.307 1 29.46 ? O1 LTT 302 B 1 
HETATM 2 C C1 LTT . . . F 3 37.609 93.529 92.349 1 27.83 ? C1 LTT 302 B 1 
HETATM 3 N N2 LTT . . . F 3 37.318 92.249 92.088 1 26.17 ? N2 LTT 302 B 1 
HETATM 4 C C3 LTT . . . F 3 36.024 91.859 92.138 1 30.16 ? C3 LTT 302 B 1 
HETATM 5 N N3 LTT . . . F 3 35.727 90.572 91.9 1 29.7 ? N3 LTT 302 B 1 
HETATM 6 C C5 LTT . . . F 3 35 92.744 92.463 1 28.11 ? C5 LTT 302 B 1 
HETATM 7 C C7 LTT . . . F 3 35.343 94.066 92.741 1 27.74 ? C7 LTT 302 B 1 
HETATM 8 N N1 LTT . . . F 3 36.624 94.458 92.682 1 28.86 ? N1 LTT 302 B 1 
HETATM 9 C C4 LTT . . . F 3 37.048 95.843 92.926 1 30.5 ? C4 LTT 302 B 1 
HETATM 10 O O3 LTT . . . F 3 35.881 96.618 93.129 1 33.63 ? O3 LTT 302 B 1 
HETATM 11 C C2 LTT . . . F 3 36 97.317 94.363 1 35.53 ? C2 LTT 302 B 1 
HETATM 12 C C8 LTT . . . F 3 34.653 97.452 95.069 1 37.21 ? C8 LTT 302 B 1 
HETATM 13 O O4 LTT . . . F 3 33.708 98.06 94.165 1 38.98 ? O4 LTT 302 B 1 
HETATM 14 O O2 LTT . . . F 3 36.974 96.628 95.149 1 34.66 ? O2 LTT 302 B 1 
HETATM 15 C C6 LTT . . . F 3 37.846 95.967 94.232 1 35.3 ? C6 LTT 302 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           15 
#