data_4ZU5
#
_model_server_result.job_id            ptaPork-dv2U9JNJHw7G4A 
_model_server_result.datetime_utc      '2024-11-26 17:43:29' 
_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          4zu5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":202}' 
#
_entry.id    4ZU5 
#
_exptl.entry_id    4ZU5 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              242.229 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            THYMIDINE 
_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            4ZU5 
_cell.length_a            93.742 
_cell.length_b            93.742 
_cell.length_c            95.623 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4ZU5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        90 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 4 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 C N N 
? 2 E N N 
#
_chem_comp.formula           'C10 H14 N2 O5' 
_chem_comp.formula_weight    242.229 
_chem_comp.id                THM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              THYMIDINE 
_chem_comp.type              'dna oh 5 prime terminus' 
_chem_comp.pdbx_synonyms     "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" 
#
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
O5' C5' THM sing 350 n n 
O5' HO5' THM sing 351 n n 
C5' C4' THM sing 352 n n 
C5' "H5'1" THM sing 353 n n 
C5' "H5'2" THM sing 354 n n 
C4' O4' THM sing 355 n n 
C4' C3' THM sing 356 n n 
C4' H4' THM sing 357 n n 
O4' C1' THM sing 358 n n 
C3' O3' THM sing 359 n n 
C3' C2' THM sing 360 n n 
C3' H3' THM sing 361 n n 
O3' HO3' THM sing 362 n n 
C2' C1' THM sing 363 n n 
C2' "H2'1" THM sing 364 n n 
C2' "H2'2" THM sing 365 n n 
C1' N1 THM sing 366 n n 
C1' H1' THM sing 367 n n 
N1 C2 THM sing 368 n n 
N1 C6 THM sing 369 n n 
C2 O2 THM doub 370 n n 
C2 N3 THM sing 371 n n 
N3 C4 THM sing 372 n n 
N3 HN3 THM sing 373 n n 
C4 O4 THM doub 374 n n 
C4 C5 THM sing 375 n n 
C5 C5M THM sing 376 n n 
C5 C6 THM doub 377 n n 
C5M HM51 THM sing 378 n n 
C5M HM52 THM sing 379 n n 
C5M HM53 THM sing 380 n n 
C6 H6 THM sing 381 n n 
#
_atom_sites.entry_id                     4ZU5 
_atom_sites.fract_transf_matrix[1][1]    0.010668 
_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]    0.010668 
_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]    0.010458 
_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 THM A 1 201 2 THM THM . 
D 3 PXN B 1 201 1 PXN PXN . 
E 2 THM B 1 202 1 THM THM . 
F 4 HOH A 1 301 66 HOH HOH . 
F 4 HOH A 2 302 49 HOH HOH . 
F 4 HOH A 3 303 29 HOH HOH . 
F 4 HOH A 4 304 67 HOH HOH . 
F 4 HOH A 5 305 13 HOH HOH . 
F 4 HOH A 6 306 52 HOH HOH . 
F 4 HOH A 7 307 21 HOH HOH . 
F 4 HOH A 8 308 55 HOH HOH . 
F 4 HOH A 9 309 25 HOH HOH . 
F 4 HOH A 10 310 65 HOH HOH . 
F 4 HOH A 11 311 2 HOH HOH . 
F 4 HOH A 12 312 51 HOH HOH . 
F 4 HOH A 13 313 30 HOH HOH . 
F 4 HOH A 14 314 16 HOH HOH . 
F 4 HOH A 15 315 82 HOH HOH . 
F 4 HOH A 16 316 7 HOH HOH . 
F 4 HOH A 17 317 59 HOH HOH . 
F 4 HOH A 18 318 48 HOH HOH . 
F 4 HOH A 19 319 50 HOH HOH . 
F 4 HOH A 20 320 24 HOH HOH . 
F 4 HOH A 21 321 63 HOH HOH . 
F 4 HOH A 22 322 64 HOH HOH . 
F 4 HOH A 23 323 1 HOH HOH . 
F 4 HOH A 24 324 26 HOH HOH . 
F 4 HOH A 25 325 11 HOH HOH . 
F 4 HOH A 26 326 27 HOH HOH . 
F 4 HOH A 27 327 9 HOH HOH . 
F 4 HOH A 28 328 32 HOH HOH . 
F 4 HOH A 29 329 62 HOH HOH . 
F 4 HOH A 30 330 12 HOH HOH . 
F 4 HOH A 31 331 58 HOH HOH . 
F 4 HOH A 32 332 20 HOH HOH . 
F 4 HOH A 33 333 56 HOH HOH . 
F 4 HOH A 34 334 4 HOH HOH . 
F 4 HOH A 35 335 81 HOH HOH . 
F 4 HOH A 36 336 28 HOH HOH . 
F 4 HOH A 37 337 23 HOH HOH . 
F 4 HOH A 38 338 10 HOH HOH . 
F 4 HOH A 39 339 15 HOH HOH . 
F 4 HOH A 40 340 46 HOH HOH . 
F 4 HOH A 41 341 31 HOH HOH . 
F 4 HOH A 42 342 57 HOH HOH . 
F 4 HOH A 43 343 80 HOH HOH . 
F 4 HOH A 44 344 22 HOH HOH . 
F 4 HOH A 45 345 60 HOH HOH . 
F 4 HOH A 46 346 54 HOH HOH . 
G 4 HOH B 1 301 6 HOH HOH . 
G 4 HOH B 2 302 84 HOH HOH . 
G 4 HOH B 3 303 78 HOH HOH . 
G 4 HOH B 4 304 37 HOH HOH . 
G 4 HOH B 5 305 70 HOH HOH . 
G 4 HOH B 6 306 14 HOH HOH . 
G 4 HOH B 7 307 33 HOH HOH . 
G 4 HOH B 8 308 8 HOH HOH . 
G 4 HOH B 9 309 36 HOH HOH . 
G 4 HOH B 10 310 75 HOH HOH . 
G 4 HOH B 11 311 19 HOH HOH . 
G 4 HOH B 12 312 40 HOH HOH . 
G 4 HOH B 13 313 72 HOH HOH . 
G 4 HOH B 14 314 43 HOH HOH . 
G 4 HOH B 15 315 69 HOH HOH . 
G 4 HOH B 16 316 79 HOH HOH . 
G 4 HOH B 17 317 3 HOH HOH . 
G 4 HOH B 18 318 47 HOH HOH . 
G 4 HOH B 19 319 76 HOH HOH . 
G 4 HOH B 20 320 17 HOH HOH . 
G 4 HOH B 21 321 41 HOH HOH . 
G 4 HOH B 22 322 34 HOH HOH . 
G 4 HOH B 23 323 74 HOH HOH . 
G 4 HOH B 24 324 83 HOH HOH . 
G 4 HOH B 25 325 85 HOH HOH . 
G 4 HOH B 26 326 71 HOH HOH . 
G 4 HOH B 27 327 35 HOH HOH . 
G 4 HOH B 28 328 39 HOH HOH . 
G 4 HOH B 29 329 77 HOH HOH . 
G 4 HOH B 30 330 38 HOH HOH . 
G 4 HOH B 31 331 42 HOH HOH . 
G 4 HOH B 32 332 5 HOH HOH . 
G 4 HOH B 33 333 44 HOH HOH . 
G 4 HOH B 34 334 73 HOH HOH . 
G 4 HOH B 35 335 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 O O5' THM . . . E 2 23.718 -3.032 3.082 0.25 34.13 ? O5' THM 202 B 1 
HETATM 2 C C5' THM . . . E 2 23.933 -3.442 4.437 0.25 32.4 ? C5' THM 202 B 1 
HETATM 3 C C4' THM . . . E 2 24.408 -2.21 5.184 0.25 32.99 ? C4' THM 202 B 1 
HETATM 4 O O4' THM . . . E 2 24.263 -2.329 6.594 0.25 32.03 ? O4' THM 202 B 1 
HETATM 5 C C3' THM . . . E 2 25.887 -1.916 5.015 0.25 32.21 ? C3' THM 202 B 1 
HETATM 6 O O3' THM . . . E 2 26.163 -1.205 3.815 0.25 33.68 ? O3' THM 202 B 1 
HETATM 7 C C2' THM . . . E 2 26.214 -1.063 6.23 0.25 32.59 ? C2' THM 202 B 1 
HETATM 8 C C1' THM . . . E 2 25.015 -1.248 7.141 0.25 32.48 ? C1' THM 202 B 1 
HETATM 9 N N1 THM . . . E 2 25.464 -1.585 8.486 0.25 33.86 ? N1 THM 202 B 1 
HETATM 10 C C2 THM . . . E 2 26.243 -0.637 9.17 0.25 34.11 ? C2 THM 202 B 1 
HETATM 11 O O2 THM . . . E 2 26.508 0.45 8.627 0.25 33.49 ? O2 THM 202 B 1 
HETATM 12 N N3 THM . . . E 2 26.702 -0.887 10.389 0.25 36.57 ? N3 THM 202 B 1 
HETATM 13 C C4 THM . . . E 2 26.401 -2.044 10.981 0.25 34.62 ? C4 THM 202 B 1 
HETATM 14 O O4 THM . . . E 2 26.865 -2.208 12.118 0.25 34.66 ? O4 THM 202 B 1 
HETATM 15 C C5 THM . . . E 2 25.568 -3.07 10.281 0.25 35.2 ? C5 THM 202 B 1 
HETATM 16 C C5M THM . . . E 2 25.194 -4.405 10.869 0.25 33.81 ? C5M THM 202 B 1 
HETATM 17 C C6 THM . . . E 2 25.126 -2.767 9.004 0.25 33.2 ? C6 THM 202 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           252 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           17 
#