data_4DWJ
#
_model_server_result.job_id            PzSkpq8cPRdZVCRdM-XWAQ 
_model_server_result.datetime_utc      '2024-11-24 04:05:45' 
_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          4dwj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":301}' 
#
_entry.id    4DWJ 
#
_exptl.entry_id    4DWJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              322.208 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-5'-PHOSPHATE" 
_entity.pdbx_number_of_molecules    7 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         81.48 
_cell.angle_beta          90.1 
_cell.angle_gamma         90.12 
_cell.entry_id            4DWJ 
_cell.length_a            58.662 
_cell.length_b            73.409 
_cell.length_c            96.868 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DWJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
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 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,P,Q 1 1 
C,D,K,L,R,S 2 1 
E,G,N,T,V 3 1 
F,H,M,O,U,W 4 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 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O 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 306 n n 
P O2P TMP sing 307 n n 
P O3P TMP sing 308 n n 
P O5' TMP sing 309 n n 
O2P HOP2 TMP sing 310 n n 
O3P HOP3 TMP sing 311 n n 
O5' C5' TMP sing 312 n n 
C5' C4' TMP sing 313 n n 
C5' "H5'1" TMP sing 314 n n 
C5' "H5'2" TMP sing 315 n n 
C4' O4' TMP sing 316 n n 
C4' C3' TMP sing 317 n n 
C4' H4' TMP sing 318 n n 
O4' C1' TMP sing 319 n n 
C3' O3' TMP sing 320 n n 
C3' C2' TMP sing 321 n n 
C3' H3' TMP sing 322 n n 
O3' HO3' TMP sing 323 n n 
C2' C1' TMP sing 324 n n 
C2' "H2'1" TMP sing 325 n n 
C2' "H2'2" TMP sing 326 n n 
C1' N1 TMP sing 327 n n 
C1' H1' TMP sing 328 n n 
N1 C2 TMP sing 329 n n 
N1 C6 TMP sing 330 n n 
C2 O2 TMP doub 331 n n 
C2 N3 TMP sing 332 n n 
N3 C4 TMP sing 333 n n 
N3 HN3 TMP sing 334 n n 
C4 O4 TMP doub 335 n n 
C4 C5 TMP sing 336 n n 
C5 C5M TMP sing 337 n n 
C5 C6 TMP doub 338 n n 
C5M H51 TMP sing 339 n n 
C5M H52 TMP sing 340 n n 
C5M H53 TMP sing 341 n n 
C6 H6 TMP sing 342 n n 
#
_atom_sites.entry_id                     4DWJ 
_atom_sites.fract_transf_matrix[1][1]    0.017047 
_atom_sites.fract_transf_matrix[1][2]    0.000035 
_atom_sites.fract_transf_matrix[1][3]    0.000024 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013622 
_atom_sites.fract_transf_matrix[2][3]    -0.002041 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.010439 
_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
I 2 TMP A 1 301 1 TMP TMP . 
J 2 TMP B 1 301 2 TMP TMP . 
K 2 TMP C 1 301 3 TMP TMP . 
L 2 TMP D 1 301 4 TMP TMP . 
M 2 TMP F 1 301 5 TMP TMP . 
N 2 TMP G 1 301 6 TMP TMP . 
O 2 TMP H 1 301 7 TMP TMP . 
P 3 HOH A 1 401 1 HOH HOH . 
P 3 HOH A 2 402 2 HOH HOH . 
P 3 HOH A 3 403 3 HOH HOH . 
P 3 HOH A 4 404 4 HOH HOH . 
P 3 HOH A 5 405 46 HOH HOH . 
P 3 HOH A 6 406 47 HOH HOH . 
P 3 HOH A 7 407 49 HOH HOH . 
P 3 HOH A 8 408 50 HOH HOH . 
P 3 HOH A 9 409 51 HOH HOH . 
P 3 HOH A 10 410 57 HOH HOH . 
P 3 HOH A 11 411 59 HOH HOH . 
Q 3 HOH B 1 401 5 HOH HOH . 
Q 3 HOH B 2 402 6 HOH HOH . 
Q 3 HOH B 3 403 7 HOH HOH . 
Q 3 HOH B 4 404 8 HOH HOH . 
Q 3 HOH B 5 405 44 HOH HOH . 
Q 3 HOH B 6 406 45 HOH HOH . 
Q 3 HOH B 7 407 48 HOH HOH . 
Q 3 HOH B 8 408 53 HOH HOH . 
Q 3 HOH B 9 409 54 HOH HOH . 
Q 3 HOH B 10 410 55 HOH HOH . 
Q 3 HOH B 11 411 69 HOH HOH . 
R 3 HOH C 1 401 9 HOH HOH . 
R 3 HOH C 2 402 10 HOH HOH . 
R 3 HOH C 3 403 11 HOH HOH . 
R 3 HOH C 4 404 12 HOH HOH . 
R 3 HOH C 5 405 13 HOH HOH . 
R 3 HOH C 6 406 56 HOH HOH . 
R 3 HOH C 7 407 58 HOH HOH . 
R 3 HOH C 8 408 65 HOH HOH . 
S 3 HOH D 1 401 14 HOH HOH . 
S 3 HOH D 2 402 15 HOH HOH . 
S 3 HOH D 3 403 16 HOH HOH . 
S 3 HOH D 4 404 17 HOH HOH . 
S 3 HOH D 5 405 18 HOH HOH . 
S 3 HOH D 6 406 19 HOH HOH . 
S 3 HOH D 7 407 20 HOH HOH . 
S 3 HOH D 8 408 21 HOH HOH . 
S 3 HOH D 9 409 22 HOH HOH . 
S 3 HOH D 10 410 25 HOH HOH . 
S 3 HOH D 11 411 26 HOH HOH . 
S 3 HOH D 12 412 27 HOH HOH . 
S 3 HOH D 13 413 28 HOH HOH . 
S 3 HOH D 14 414 29 HOH HOH . 
S 3 HOH D 15 415 36 HOH HOH . 
S 3 HOH D 16 416 60 HOH HOH . 
S 3 HOH D 17 417 70 HOH HOH . 
S 3 HOH D 18 418 71 HOH HOH . 
T 3 HOH E 1 301 31 HOH HOH . 
T 3 HOH E 2 302 32 HOH HOH . 
T 3 HOH E 3 303 33 HOH HOH . 
T 3 HOH E 4 304 34 HOH HOH . 
T 3 HOH E 5 305 35 HOH HOH . 
T 3 HOH E 6 306 37 HOH HOH . 
T 3 HOH E 7 307 61 HOH HOH . 
T 3 HOH E 8 308 62 HOH HOH . 
T 3 HOH E 9 309 63 HOH HOH . 
U 3 HOH F 1 401 38 HOH HOH . 
U 3 HOH F 2 402 64 HOH HOH . 
U 3 HOH F 3 403 66 HOH HOH . 
V 3 HOH G 1 401 39 HOH HOH . 
V 3 HOH G 2 402 40 HOH HOH . 
V 3 HOH G 3 403 41 HOH HOH . 
V 3 HOH G 4 404 42 HOH HOH . 
V 3 HOH G 5 405 43 HOH HOH . 
V 3 HOH G 6 406 52 HOH HOH . 
V 3 HOH G 7 407 67 HOH HOH . 
V 3 HOH G 8 408 68 HOH HOH . 
W 3 HOH H 1 401 23 HOH HOH . 
W 3 HOH H 2 402 24 HOH HOH . 
W 3 HOH H 3 403 30 HOH HOH . 
W 3 HOH H 4 404 72 HOH HOH . 
W 3 HOH H 5 405 73 HOH HOH . 
W 3 HOH H 6 406 74 HOH HOH . 
W 3 HOH H 7 407 75 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 2 -5.559 -71.104 -3.75 1 131.68 ? P TMP 301 B 1 
HETATM 2 O O1P TMP . . . J 2 -6.729 -72.057 -3.638 1 149.47 ? O1P TMP 301 B 1 
HETATM 3 O O2P TMP . . . J 2 -4.235 -71.789 -3.989 1 133.53 ? O2P TMP 301 B 1 
HETATM 4 O O3P TMP . . . J 2 -5.547 -70.004 -2.703 1 95.9 ? O3P TMP 301 B 1 
HETATM 5 O O5' TMP . . . J 2 -5.816 -70.356 -5.15 1 105.76 ? O5' TMP 301 B 1 
HETATM 6 N N1 TMP . . . J 2 -2.208 -65.864 -7.961 1 80.21 ? N1 TMP 301 B 1 
HETATM 7 C C2 TMP . . . J 2 -1.886 -64.887 -8.918 1 68.11 ? C2 TMP 301 B 1 
HETATM 8 O O2 TMP . . . J 2 -2.334 -65.003 -10.077 1 83.18 ? O2 TMP 301 B 1 
HETATM 9 N N3 TMP . . . J 2 -1.087 -63.856 -8.61 1 60.34 ? N3 TMP 301 B 1 
HETATM 10 C C4 TMP . . . J 2 -0.589 -63.693 -7.392 1 47.19 ? C4 TMP 301 B 1 
HETATM 11 O O4 TMP . . . J 2 0.087 -62.701 -7.152 1 44.7 ? O4 TMP 301 B 1 
HETATM 12 C C5 TMP . . . J 2 -0.918 -64.672 -6.357 1 66.67 ? C5 TMP 301 B 1 
HETATM 13 C C5M TMP . . . J 2 -0.406 -64.539 -4.954 1 80.3 ? C5M TMP 301 B 1 
HETATM 14 C C6 TMP . . . J 2 -1.731 -65.746 -6.713 1 91.25 ? C6 TMP 301 B 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           14 
#