data_3UDG
#
_model_server_result.job_id            5vHAHwm9qQhz00dM4bzzTA 
_model_server_result.datetime_utc      '2024-10-14 05:25:21' 
_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          3udg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":302}' 
#
_entry.id    3UDG 
#
_exptl.entry_id    3UDG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              322.208 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-5'-PHOSPHATE" 
_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          94.12 
_cell.angle_gamma         90 
_cell.entry_id            3UDG 
_cell.length_a            161.144 
_cell.length_b            95.675 
_cell.length_c            65.726 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3UDG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? hexameric 6 author_defined_assembly 1 
? hexameric 6 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,H,J,N,S 1 1,2 
B,C,D,E,F,I,K,L,M,O,P,Q,R 2 1 
#
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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
#
_chem_comp.formula           'C10 H15 N2 O8 P' 
_chem_comp.formula_weight    322.208 
_chem_comp.id                TMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-5'-PHOSPHATE" 
_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
P O1P TMP doub 330 n n 
P O2P TMP sing 331 n n 
P O3P TMP sing 332 n n 
P O5' TMP sing 333 n n 
O2P HOP2 TMP sing 334 n n 
O3P HOP3 TMP sing 335 n n 
O5' C5' TMP sing 336 n n 
C5' C4' TMP sing 337 n n 
C5' "H5'1" TMP sing 338 n n 
C5' "H5'2" TMP sing 339 n n 
C4' O4' TMP sing 340 n n 
C4' C3' TMP sing 341 n n 
C4' H4' TMP sing 342 n n 
O4' C1' TMP sing 343 n n 
C3' O3' TMP sing 344 n n 
C3' C2' TMP sing 345 n n 
C3' H3' TMP sing 346 n n 
O3' HO3' TMP sing 347 n n 
C2' C1' TMP sing 348 n n 
C2' "H2'1" TMP sing 349 n n 
C2' "H2'2" TMP sing 350 n n 
C1' N1 TMP sing 351 n n 
C1' H1' TMP sing 352 n n 
N1 C2 TMP sing 353 n n 
N1 C6 TMP sing 354 n n 
C2 O2 TMP doub 355 n n 
C2 N3 TMP sing 356 n n 
N3 C4 TMP sing 357 n n 
N3 HN3 TMP sing 358 n n 
C4 O4 TMP doub 359 n n 
C4 C5 TMP sing 360 n n 
C5 C5M TMP sing 361 n n 
C5 C6 TMP doub 362 n n 
C5M H51 TMP sing 363 n n 
C5M H52 TMP sing 364 n n 
C5M H53 TMP sing 365 n n 
C6 H6 TMP sing 366 n n 
#
_atom_sites.entry_id                     3UDG 
_atom_sites.fract_transf_matrix[1][1]    0.006206 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000447 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010452 
_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]    0.015254 
_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
J 3 TMP A 1 302 1 TMP TMP . 
K 3 TMP B 1 302 1 TMP TMP . 
L 3 TMP B 1 303 1 TMP TMP . 
M 3 TMP C 1 302 1 TMP TMP . 
N 4 HOH A 1 303 1 HOH HOH . 
N 4 HOH A 2 304 2 HOH HOH . 
N 4 HOH A 3 305 3 HOH HOH . 
N 4 HOH A 4 306 4 HOH HOH . 
N 4 HOH A 5 307 6 HOH HOH . 
N 4 HOH A 6 308 7 HOH HOH . 
N 4 HOH A 7 309 8 HOH HOH . 
N 4 HOH A 8 310 9 HOH HOH . 
N 4 HOH A 9 311 10 HOH HOH . 
N 4 HOH A 10 312 11 HOH HOH . 
N 4 HOH A 11 313 12 HOH HOH . 
N 4 HOH A 12 314 13 HOH HOH . 
N 4 HOH A 13 315 14 HOH HOH . 
N 4 HOH A 14 316 15 HOH HOH . 
N 4 HOH A 15 317 16 HOH HOH . 
N 4 HOH A 16 318 17 HOH HOH . 
N 4 HOH A 17 319 18 HOH HOH . 
N 4 HOH A 18 320 19 HOH HOH . 
N 4 HOH A 19 321 20 HOH HOH . 
N 4 HOH A 20 322 21 HOH HOH . 
N 4 HOH A 21 323 22 HOH HOH . 
N 4 HOH A 22 324 24 HOH HOH . 
N 4 HOH A 23 325 25 HOH HOH . 
N 4 HOH A 24 326 26 HOH HOH . 
N 4 HOH A 25 327 27 HOH HOH . 
N 4 HOH A 26 328 28 HOH HOH . 
N 4 HOH A 27 329 29 HOH HOH . 
N 4 HOH A 28 330 30 HOH HOH . 
N 4 HOH A 29 331 31 HOH HOH . 
N 4 HOH A 30 332 36 HOH HOH . 
N 4 HOH A 31 333 83 HOH HOH . 
N 4 HOH A 32 334 84 HOH HOH . 
N 4 HOH A 33 335 85 HOH HOH . 
N 4 HOH A 34 336 87 HOH HOH . 
N 4 HOH A 35 337 100 HOH HOH . 
N 4 HOH A 36 338 101 HOH HOH . 
N 4 HOH A 37 339 106 HOH HOH . 
N 4 HOH A 38 340 107 HOH HOH . 
N 4 HOH A 39 341 5 HOH HOH . 
O 4 HOH B 1 304 23 HOH HOH . 
O 4 HOH B 2 305 32 HOH HOH . 
O 4 HOH B 3 306 33 HOH HOH . 
O 4 HOH B 4 307 37 HOH HOH . 
O 4 HOH B 5 308 39 HOH HOH . 
O 4 HOH B 6 309 40 HOH HOH . 
O 4 HOH B 7 310 41 HOH HOH . 
O 4 HOH B 8 311 42 HOH HOH . 
O 4 HOH B 9 312 43 HOH HOH . 
O 4 HOH B 10 313 44 HOH HOH . 
O 4 HOH B 11 314 45 HOH HOH . 
O 4 HOH B 12 315 46 HOH HOH . 
O 4 HOH B 13 316 47 HOH HOH . 
O 4 HOH B 14 317 48 HOH HOH . 
O 4 HOH B 15 318 49 HOH HOH . 
O 4 HOH B 16 319 50 HOH HOH . 
O 4 HOH B 17 320 71 HOH HOH . 
O 4 HOH B 18 321 72 HOH HOH . 
O 4 HOH B 19 322 74 HOH HOH . 
O 4 HOH B 20 323 75 HOH HOH . 
O 4 HOH B 21 324 76 HOH HOH . 
O 4 HOH B 22 325 77 HOH HOH . 
O 4 HOH B 23 326 78 HOH HOH . 
O 4 HOH B 24 327 79 HOH HOH . 
O 4 HOH B 25 328 80 HOH HOH . 
O 4 HOH B 26 329 81 HOH HOH . 
O 4 HOH B 27 330 82 HOH HOH . 
O 4 HOH B 28 331 88 HOH HOH . 
O 4 HOH B 29 332 89 HOH HOH . 
O 4 HOH B 30 333 90 HOH HOH . 
O 4 HOH B 31 334 94 HOH HOH . 
O 4 HOH B 32 335 95 HOH HOH . 
O 4 HOH B 33 336 98 HOH HOH . 
O 4 HOH B 34 337 102 HOH HOH . 
O 4 HOH B 35 338 103 HOH HOH . 
O 4 HOH B 36 339 70 HOH HOH . 
O 4 HOH B 37 340 91 HOH HOH . 
P 4 HOH C 1 303 35 HOH HOH . 
P 4 HOH C 2 304 38 HOH HOH . 
P 4 HOH C 3 305 51 HOH HOH . 
P 4 HOH C 4 306 52 HOH HOH . 
P 4 HOH C 5 307 53 HOH HOH . 
P 4 HOH C 6 308 54 HOH HOH . 
P 4 HOH C 7 309 55 HOH HOH . 
P 4 HOH C 8 310 56 HOH HOH . 
P 4 HOH C 9 311 57 HOH HOH . 
P 4 HOH C 10 312 58 HOH HOH . 
P 4 HOH C 11 313 59 HOH HOH . 
P 4 HOH C 12 314 60 HOH HOH . 
P 4 HOH C 13 315 61 HOH HOH . 
P 4 HOH C 14 316 62 HOH HOH . 
P 4 HOH C 15 317 63 HOH HOH . 
P 4 HOH C 16 318 64 HOH HOH . 
P 4 HOH C 17 319 65 HOH HOH . 
P 4 HOH C 18 320 66 HOH HOH . 
P 4 HOH C 19 321 67 HOH HOH . 
P 4 HOH C 20 322 68 HOH HOH . 
P 4 HOH C 21 323 69 HOH HOH . 
P 4 HOH C 22 324 97 HOH HOH . 
P 4 HOH C 23 325 105 HOH HOH . 
Q 4 HOH D 1 96 96 HOH HOH . 
R 4 HOH E 1 36 34 HOH HOH . 
R 4 HOH E 2 73 73 HOH HOH . 
R 4 HOH E 3 92 92 HOH HOH . 
R 4 HOH E 4 93 93 HOH HOH . 
R 4 HOH E 5 104 104 HOH HOH . 
S 4 HOH G 1 86 86 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 P P TMP . . . J 3 24.435 -22.528 -1.138 1 123.97 ? P TMP 302 A 1 
HETATM 2 O O1P TMP . . . J 3 23.324 -21.728 -1.801 1 112.6 ? O1P TMP 302 A 1 
HETATM 3 O O2P TMP . . . J 3 24.551 -23.956 -1.619 1 120.85 ? O2P TMP 302 A 1 
HETATM 4 O O3P TMP . . . J 3 24.455 -22.46 0.372 1 116.02 ? O3P TMP 302 A 1 
HETATM 5 O O5' TMP . . . J 3 25.807 -21.822 -1.661 1 112.47 ? O5' TMP 302 A 1 
HETATM 6 C C5' TMP . . . J 3 26.143 -20.455 -1.402 1 105.74 ? C5' TMP 302 A 1 
HETATM 7 C C4' TMP . . . J 3 25.906 -19.543 -2.599 1 110.2 ? C4' TMP 302 A 1 
HETATM 8 O O4' TMP . . . J 3 25.127 -18.403 -2.211 1 116.82 ? O4' TMP 302 A 1 
HETATM 9 C C3' TMP . . . J 3 27.202 -18.962 -3.151 1 119.07 ? C3' TMP 302 A 1 
HETATM 10 O O3' TMP . . . J 3 27.567 -19.633 -4.357 1 117.93 ? O3' TMP 302 A 1 
HETATM 11 C C2' TMP . . . J 3 26.946 -17.49 -3.441 1 116.43 ? C2' TMP 302 A 1 
HETATM 12 C C1' TMP . . . J 3 25.509 -17.248 -2.984 1 115.66 ? C1' TMP 302 A 1 
HETATM 13 N N1 TMP . . . J 3 25.376 -15.974 -2.24 1 108.73 ? N1 TMP 302 A 1 
HETATM 14 C C2 TMP . . . J 3 24.663 -14.876 -2.818 1 100.59 ? C2 TMP 302 A 1 
HETATM 15 O O2 TMP . . . J 3 24.133 -14.975 -3.954 1 89.86 ? O2 TMP 302 A 1 
HETATM 16 N N3 TMP . . . J 3 24.538 -13.708 -2.156 1 101.99 ? N3 TMP 302 A 1 
HETATM 17 C C4 TMP . . . J 3 25.073 -13.534 -0.933 1 101.22 ? C4 TMP 302 A 1 
HETATM 18 O O4 TMP . . . J 3 24.941 -12.44 -0.331 1 97.46 ? O4 TMP 302 A 1 
HETATM 19 C C5 TMP . . . J 3 25.821 -14.663 -0.309 1 97.11 ? C5 TMP 302 A 1 
HETATM 20 C C5M TMP . . . J 3 26.444 -14.528 1.05 1 94.37 ? C5M TMP 302 A 1 
HETATM 21 C C6 TMP . . . J 3 25.939 -15.854 -1.017 1 105.27 ? C6 TMP 302 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           21 
#