data_2PAK
#
_model_server_result.job_id            jb-D0fR9o5jhOrwJsdgE4A 
_model_server_result.datetime_utc      '2024-10-12 15:27:10' 
_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          2pak 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":140}' 
#
_entry.id    2PAK 
#
_exptl.entry_id    2PAK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-5'-DIPHOSPHATE" 
_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            2PAK 
_cell.length_a            61.3 
_cell.length_b            61.3 
_cell.length_c            201.4 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2PAK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 D N N 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                TYD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-5'-DIPHOSPHATE" 
_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
PA O1A TYD doub 334 n n 
PA O2A TYD sing 335 n n 
PA O3A TYD sing 336 n n 
PA O5' TYD sing 337 n n 
O2A HOA2 TYD sing 338 n n 
O3A PB TYD sing 339 n n 
PB O1B TYD doub 340 n n 
PB O2B TYD sing 341 n n 
PB O3B TYD sing 342 n n 
O2B HOB2 TYD sing 343 n n 
O3B HOB3 TYD sing 344 n n 
O5' C5' TYD sing 345 n n 
C5' C4' TYD sing 346 n n 
C5' "H5'1" TYD sing 347 n n 
C5' "H5'2" TYD sing 348 n n 
C4' O4' TYD sing 349 n n 
C4' C3' TYD sing 350 n n 
C4' H4' TYD sing 351 n n 
O4' C1' TYD sing 352 n n 
C3' O3' TYD sing 353 n n 
C3' C2' TYD sing 354 n n 
C3' H3' TYD sing 355 n n 
O3' HO3' TYD sing 356 n n 
C2' C1' TYD sing 357 n n 
C2' "H2'1" TYD sing 358 n n 
C2' "H2'2" TYD sing 359 n n 
C1' N1 TYD sing 360 n n 
C1' H1' TYD sing 361 n n 
N1 C2 TYD sing 362 n y 
N1 C6 TYD sing 363 n y 
C2 O2 TYD doub 364 n n 
C2 N3 TYD sing 365 n y 
N3 C4 TYD sing 366 n y 
N3 HN3 TYD sing 367 n n 
C4 O4 TYD doub 368 n n 
C4 C5 TYD sing 369 n y 
C5 C5M TYD sing 370 n n 
C5 C6 TYD doub 371 n y 
C5M H51 TYD sing 372 n n 
C5M H52 TYD sing 373 n n 
C5M H53 TYD sing 374 n n 
C6 H6 TYD sing 375 n n 
#
_atom_sites.entry_id                     2PAK 
_atom_sites.fract_transf_matrix[1][1]    0.016313 
_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]    0.016313 
_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]    0.004965 
_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 TYD A 1 140 1 TYD TDP . 
D 2 TYD B 1 140 2 TYD TDP . 
E 3 HOH A 1 141 3 HOH HOH . 
E 3 HOH A 2 142 4 HOH HOH . 
E 3 HOH A 3 143 5 HOH HOH . 
E 3 HOH A 4 144 6 HOH HOH . 
E 3 HOH A 5 145 7 HOH HOH . 
E 3 HOH A 6 146 8 HOH HOH . 
E 3 HOH A 7 147 9 HOH HOH . 
E 3 HOH A 8 148 10 HOH HOH . 
E 3 HOH A 9 149 11 HOH HOH . 
E 3 HOH A 10 150 12 HOH HOH . 
E 3 HOH A 11 151 13 HOH HOH . 
E 3 HOH A 12 152 14 HOH HOH . 
E 3 HOH A 13 153 15 HOH HOH . 
E 3 HOH A 14 154 16 HOH HOH . 
E 3 HOH A 15 155 19 HOH HOH . 
E 3 HOH A 16 156 20 HOH HOH . 
E 3 HOH A 17 157 21 HOH HOH . 
E 3 HOH A 18 158 22 HOH HOH . 
E 3 HOH A 19 159 23 HOH HOH . 
E 3 HOH A 20 160 24 HOH HOH . 
E 3 HOH A 21 161 25 HOH HOH . 
E 3 HOH A 22 162 26 HOH HOH . 
E 3 HOH A 23 163 28 HOH HOH . 
E 3 HOH A 24 164 29 HOH HOH . 
E 3 HOH A 25 165 31 HOH HOH . 
E 3 HOH A 26 166 32 HOH HOH . 
E 3 HOH A 27 167 33 HOH HOH . 
E 3 HOH A 28 168 35 HOH HOH . 
E 3 HOH A 29 169 36 HOH HOH . 
E 3 HOH A 30 170 38 HOH HOH . 
E 3 HOH A 31 171 39 HOH HOH . 
E 3 HOH A 32 172 40 HOH HOH . 
E 3 HOH A 33 173 41 HOH HOH . 
E 3 HOH A 34 174 42 HOH HOH . 
E 3 HOH A 35 175 43 HOH HOH . 
E 3 HOH A 36 176 44 HOH HOH . 
E 3 HOH A 37 177 45 HOH HOH . 
E 3 HOH A 38 178 46 HOH HOH . 
E 3 HOH A 39 179 47 HOH HOH . 
E 3 HOH A 40 180 48 HOH HOH . 
E 3 HOH A 41 181 49 HOH HOH . 
E 3 HOH A 42 182 50 HOH HOH . 
E 3 HOH A 43 183 51 HOH HOH . 
E 3 HOH A 44 184 52 HOH HOH . 
E 3 HOH A 45 185 53 HOH HOH . 
E 3 HOH A 46 186 55 HOH HOH . 
E 3 HOH A 47 187 56 HOH HOH . 
E 3 HOH A 48 188 57 HOH HOH . 
E 3 HOH A 49 189 58 HOH HOH . 
E 3 HOH A 50 190 59 HOH HOH . 
E 3 HOH A 51 191 60 HOH HOH . 
E 3 HOH A 52 192 61 HOH HOH . 
E 3 HOH A 53 193 62 HOH HOH . 
E 3 HOH A 54 194 63 HOH HOH . 
E 3 HOH A 55 195 65 HOH HOH . 
E 3 HOH A 56 196 66 HOH HOH . 
E 3 HOH A 57 197 67 HOH HOH . 
E 3 HOH A 58 198 68 HOH HOH . 
E 3 HOH A 59 199 97 HOH HOH . 
E 3 HOH A 60 200 98 HOH HOH . 
E 3 HOH A 61 201 99 HOH HOH . 
E 3 HOH A 62 202 100 HOH HOH . 
E 3 HOH A 63 203 101 HOH HOH . 
E 3 HOH A 64 204 103 HOH HOH . 
E 3 HOH A 65 205 104 HOH HOH . 
E 3 HOH A 66 206 105 HOH HOH . 
E 3 HOH A 67 207 106 HOH HOH . 
E 3 HOH A 68 208 107 HOH HOH . 
E 3 HOH A 69 209 108 HOH HOH . 
E 3 HOH A 70 210 109 HOH HOH . 
E 3 HOH A 71 211 110 HOH HOH . 
E 3 HOH A 72 212 111 HOH HOH . 
E 3 HOH A 73 213 112 HOH HOH . 
E 3 HOH A 74 214 113 HOH HOH . 
E 3 HOH A 75 215 121 HOH HOH . 
E 3 HOH A 76 216 123 HOH HOH . 
F 3 HOH B 1 141 17 HOH HOH . 
F 3 HOH B 2 142 18 HOH HOH . 
F 3 HOH B 3 143 27 HOH HOH . 
F 3 HOH B 4 144 30 HOH HOH . 
F 3 HOH B 5 145 34 HOH HOH . 
F 3 HOH B 6 146 37 HOH HOH . 
F 3 HOH B 7 147 54 HOH HOH . 
F 3 HOH B 8 148 64 HOH HOH . 
F 3 HOH B 9 149 69 HOH HOH . 
F 3 HOH B 10 150 70 HOH HOH . 
F 3 HOH B 11 151 71 HOH HOH . 
F 3 HOH B 12 152 72 HOH HOH . 
F 3 HOH B 13 153 73 HOH HOH . 
F 3 HOH B 14 154 74 HOH HOH . 
F 3 HOH B 15 155 75 HOH HOH . 
F 3 HOH B 16 156 76 HOH HOH . 
F 3 HOH B 17 157 77 HOH HOH . 
F 3 HOH B 18 158 78 HOH HOH . 
F 3 HOH B 19 159 79 HOH HOH . 
F 3 HOH B 20 160 80 HOH HOH . 
F 3 HOH B 21 161 81 HOH HOH . 
F 3 HOH B 22 162 82 HOH HOH . 
F 3 HOH B 23 163 83 HOH HOH . 
F 3 HOH B 24 164 84 HOH HOH . 
F 3 HOH B 25 165 85 HOH HOH . 
F 3 HOH B 26 166 86 HOH HOH . 
F 3 HOH B 27 167 87 HOH HOH . 
F 3 HOH B 28 168 88 HOH HOH . 
F 3 HOH B 29 169 89 HOH HOH . 
F 3 HOH B 30 170 90 HOH HOH . 
F 3 HOH B 31 171 91 HOH HOH . 
F 3 HOH B 32 172 92 HOH HOH . 
F 3 HOH B 33 173 93 HOH HOH . 
F 3 HOH B 34 174 94 HOH HOH . 
F 3 HOH B 35 175 95 HOH HOH . 
F 3 HOH B 36 176 96 HOH HOH . 
F 3 HOH B 37 177 102 HOH HOH . 
F 3 HOH B 38 178 114 HOH HOH . 
F 3 HOH B 39 179 115 HOH HOH . 
F 3 HOH B 40 180 116 HOH HOH . 
F 3 HOH B 41 181 117 HOH HOH . 
F 3 HOH B 42 182 118 HOH HOH . 
F 3 HOH B 43 183 119 HOH HOH . 
F 3 HOH B 44 184 120 HOH HOH . 
F 3 HOH B 45 185 122 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 PA TYD . . . D 2 -6.768 43.08 51.178 1 94.62 ? PA TYD 140 B 1 
HETATM 2 O O1A TYD . . . D 2 -7.338 41.742 51.476 1 53.19 ? O1A TYD 140 B 1 
HETATM 3 O O2A TYD . . . D 2 -5.284 43.093 51.236 1 55.52 ? O2A TYD 140 B 1 
HETATM 4 O O3A TYD . . . D 2 -7.42 44.162 52.223 1 100 ? O3A TYD 140 B 1 
HETATM 5 P PB TYD . . . D 2 -7.386 45.711 52.244 1 82.62 ? PB TYD 140 B 1 
HETATM 6 O O1B TYD . . . D 2 -8.75 46.23 52.015 1 75.86 ? O1B TYD 140 B 1 
HETATM 7 O O2B TYD . . . D 2 -6.49 46.166 51.162 1 56.46 ? O2B TYD 140 B 1 
HETATM 8 O O3B TYD . . . D 2 -6.874 46.185 53.548 1 89.81 ? O3B TYD 140 B 1 
HETATM 9 O O5' TYD . . . D 2 -7.369 43.839 49.899 1 35.33 ? O5' TYD 140 B 1 
HETATM 10 C C5' TYD . . . D 2 -6.655 43.824 48.658 1 18.87 ? C5' TYD 140 B 1 
HETATM 11 C C4' TYD . . . D 2 -7.614 43.783 47.474 1 34.69 ? C4' TYD 140 B 1 
HETATM 12 O O4' TYD . . . D 2 -7.588 42.461 46.823 1 62.25 ? O4' TYD 140 B 1 
HETATM 13 C C3' TYD . . . D 2 -9.085 44.086 47.772 1 45.75 ? C3' TYD 140 B 1 
HETATM 14 O O3' TYD . . . D 2 -9.85 44.664 46.693 1 38.9 ? O3' TYD 140 B 1 
HETATM 15 C C2' TYD . . . D 2 -9.57 42.671 47.968 1 49.06 ? C2' TYD 140 B 1 
HETATM 16 C C1' TYD . . . D 2 -8.906 41.976 46.795 1 65.42 ? C1' TYD 140 B 1 
HETATM 17 N N1 TYD . . . D 2 -8.99 40.541 47.05 1 55.71 ? N1 TYD 140 B 1 
HETATM 18 C C2 TYD . . . D 2 -9.855 39.766 46.323 1 32.48 ? C2 TYD 140 B 1 
HETATM 19 O O2 TYD . . . D 2 -10.572 40.191 45.435 1 34.61 ? O2 TYD 140 B 1 
HETATM 20 N N3 TYD . . . D 2 -9.891 38.446 46.681 1 24.89 ? N3 TYD 140 B 1 
HETATM 21 C C4 TYD . . . D 2 -9.153 37.839 47.683 1 13.28 ? C4 TYD 140 B 1 
HETATM 22 O O4 TYD . . . D 2 -9.292 36.647 47.892 1 37.75 ? O4 TYD 140 B 1 
HETATM 23 C C5 TYD . . . D 2 -8.295 38.729 48.375 1 29.1 ? C5 TYD 140 B 1 
HETATM 24 C C5M TYD . . . D 2 -7.425 38.223 49.525 1 19.08 ? C5M TYD 140 B 1 
HETATM 25 C C6 TYD . . . D 2 -8.233 39.997 48.061 1 34.08 ? C6 TYD 140 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#