data_1NDC
#
_model_server_result.job_id            CQomrMQUkrMTkwG6fzRT3w 
_model_server_result.datetime_utc      '2024-10-18 23:26:15' 
_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          1ndc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":160}' 
#
_entry.id    1NDC 
#
_exptl.entry_id    1NDC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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         120 
_cell.entry_id            1NDC 
_cell.length_a            79.8 
_cell.length_b            79.8 
_cell.length_c            160.6 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1NDC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4,5,6 
#
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 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 
5 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
6 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 C O1A TYD . A TYD 160 1_555 B MG MG . A MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc2 C O2B TYD . A TYD 160 1_555 B MG MG . A MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc3 B MG MG . A MG 161 1_555 D O HOH . A HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? 
metalc ? metalc4 B MG MG . A MG 161 1_555 D O HOH . A HOH 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? 
metalc ? metalc5 B MG MG . A MG 161 1_555 D O HOH . A HOH 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? 
metalc ? metalc6 B MG MG . A MG 161 1_555 D O HOH . A HOH 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
#
_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 321 n n 
PA O2A TYD sing 322 n n 
PA O3A TYD sing 323 n n 
PA O5' TYD sing 324 n n 
O2A HOA2 TYD sing 325 n n 
O3A PB TYD sing 326 n n 
PB O1B TYD doub 327 n n 
PB O2B TYD sing 328 n n 
PB O3B TYD sing 329 n n 
O2B HOB2 TYD sing 330 n n 
O3B HOB3 TYD sing 331 n n 
O5' C5' TYD sing 332 n n 
C5' C4' TYD sing 333 n n 
C5' "H5'1" TYD sing 334 n n 
C5' "H5'2" TYD sing 335 n n 
C4' O4' TYD sing 336 n n 
C4' C3' TYD sing 337 n n 
C4' H4' TYD sing 338 n n 
O4' C1' TYD sing 339 n n 
C3' O3' TYD sing 340 n n 
C3' C2' TYD sing 341 n n 
C3' H3' TYD sing 342 n n 
O3' HO3' TYD sing 343 n n 
C2' C1' TYD sing 344 n n 
C2' "H2'1" TYD sing 345 n n 
C2' "H2'2" TYD sing 346 n n 
C1' N1 TYD sing 347 n n 
C1' H1' TYD sing 348 n n 
N1 C2 TYD sing 349 n y 
N1 C6 TYD sing 350 n y 
C2 O2 TYD doub 351 n n 
C2 N3 TYD sing 352 n y 
N3 C4 TYD sing 353 n y 
N3 HN3 TYD sing 354 n n 
C4 O4 TYD doub 355 n n 
C4 C5 TYD sing 356 n y 
C5 C5M TYD sing 357 n n 
C5 C6 TYD doub 358 n y 
C5M H51 TYD sing 359 n n 
C5M H52 TYD sing 360 n n 
C5M H53 TYD sing 361 n n 
C6 H6 TYD sing 362 n n 
#
_atom_sites.entry_id                     1NDC 
_atom_sites.fract_transf_matrix[1][1]    0.012531 
_atom_sites.fract_transf_matrix[1][2]    0.007235 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01447 
_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]    0.006227 
_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
B 2 MG A 1 161 161 MG MG . 
C 3 TYD A 1 160 160 TYD TYD . 
D 4 HOH A 1 200 200 HOH HOH . 
D 4 HOH A 2 201 201 HOH HOH . 
D 4 HOH A 3 202 202 HOH HOH . 
D 4 HOH A 4 203 203 HOH HOH . 
D 4 HOH A 5 204 204 HOH HOH . 
D 4 HOH A 6 205 205 HOH HOH . 
D 4 HOH A 7 206 206 HOH HOH . 
D 4 HOH A 8 207 207 HOH HOH . 
D 4 HOH A 9 208 208 HOH HOH . 
D 4 HOH A 10 209 209 HOH HOH . 
D 4 HOH A 11 210 210 HOH HOH . 
D 4 HOH A 12 211 211 HOH HOH . 
D 4 HOH A 13 212 212 HOH HOH . 
D 4 HOH A 14 213 213 HOH HOH . 
D 4 HOH A 15 214 214 HOH HOH . 
D 4 HOH A 16 215 215 HOH HOH . 
D 4 HOH A 17 216 216 HOH HOH . 
D 4 HOH A 18 217 217 HOH HOH . 
D 4 HOH A 19 218 218 HOH HOH . 
D 4 HOH A 20 219 219 HOH HOH . 
D 4 HOH A 21 220 220 HOH HOH . 
D 4 HOH A 22 221 221 HOH HOH . 
D 4 HOH A 23 222 222 HOH HOH . 
D 4 HOH A 24 223 223 HOH HOH . 
D 4 HOH A 25 224 224 HOH HOH . 
D 4 HOH A 26 225 225 HOH HOH . 
D 4 HOH A 27 226 226 HOH HOH . 
D 4 HOH A 28 227 227 HOH HOH . 
D 4 HOH A 29 228 228 HOH HOH . 
D 4 HOH A 30 229 229 HOH HOH . 
D 4 HOH A 31 230 230 HOH HOH . 
D 4 HOH A 32 231 231 HOH HOH . 
D 4 HOH A 33 232 232 HOH HOH . 
D 4 HOH A 34 233 233 HOH HOH . 
D 4 HOH A 35 234 234 HOH HOH . 
D 4 HOH A 36 235 235 HOH HOH . 
D 4 HOH A 37 236 236 HOH HOH . 
D 4 HOH A 38 237 237 HOH HOH . 
D 4 HOH A 39 238 238 HOH HOH . 
D 4 HOH A 40 239 239 HOH HOH . 
D 4 HOH A 41 240 240 HOH HOH . 
D 4 HOH A 42 241 241 HOH HOH . 
D 4 HOH A 43 242 242 HOH HOH . 
D 4 HOH A 44 243 243 HOH HOH . 
D 4 HOH A 45 244 244 HOH HOH . 
D 4 HOH A 46 245 245 HOH HOH . 
D 4 HOH A 47 246 246 HOH HOH . 
D 4 HOH A 48 247 247 HOH HOH . 
D 4 HOH A 49 248 248 HOH HOH . 
D 4 HOH A 50 249 249 HOH HOH . 
D 4 HOH A 51 250 250 HOH HOH . 
D 4 HOH A 52 251 251 HOH HOH . 
D 4 HOH A 53 252 252 HOH HOH . 
D 4 HOH A 54 253 253 HOH HOH . 
D 4 HOH A 55 254 254 HOH HOH . 
D 4 HOH A 56 255 255 HOH HOH . 
D 4 HOH A 57 256 256 HOH HOH . 
D 4 HOH A 58 257 257 HOH HOH . 
D 4 HOH A 59 258 258 HOH HOH . 
D 4 HOH A 60 259 259 HOH HOH . 
D 4 HOH A 61 260 260 HOH HOH . 
D 4 HOH A 62 261 261 HOH HOH . 
D 4 HOH A 63 262 262 HOH HOH . 
D 4 HOH A 64 263 263 HOH HOH . 
D 4 HOH A 65 264 264 HOH HOH . 
D 4 HOH A 66 265 265 HOH HOH . 
D 4 HOH A 67 266 266 HOH HOH . 
D 4 HOH A 68 267 267 HOH HOH . 
D 4 HOH A 69 268 268 HOH HOH . 
D 4 HOH A 70 269 269 HOH HOH . 
D 4 HOH A 71 270 270 HOH HOH . 
D 4 HOH A 72 271 271 HOH HOH . 
D 4 HOH A 73 272 272 HOH HOH . 
D 4 HOH A 74 273 273 HOH HOH . 
D 4 HOH A 75 274 274 HOH HOH . 
D 4 HOH A 76 275 275 HOH HOH . 
D 4 HOH A 77 276 276 HOH HOH . 
D 4 HOH A 78 277 277 HOH HOH . 
D 4 HOH A 79 278 278 HOH HOH . 
D 4 HOH A 80 279 279 HOH HOH . 
D 4 HOH A 81 280 280 HOH HOH . 
D 4 HOH A 82 281 281 HOH HOH . 
D 4 HOH A 83 282 282 HOH HOH . 
D 4 HOH A 84 283 283 HOH HOH . 
D 4 HOH A 85 284 284 HOH HOH . 
D 4 HOH A 86 285 285 HOH HOH . 
D 4 HOH A 87 286 286 HOH HOH . 
D 4 HOH A 88 287 287 HOH HOH . 
D 4 HOH A 89 288 288 HOH HOH . 
D 4 HOH A 90 289 289 HOH HOH . 
D 4 HOH A 91 290 290 HOH HOH . 
D 4 HOH A 92 291 291 HOH HOH . 
D 4 HOH A 93 292 292 HOH HOH . 
D 4 HOH A 94 293 293 HOH HOH . 
D 4 HOH A 95 294 294 HOH HOH . 
D 4 HOH A 96 295 295 HOH HOH . 
D 4 HOH A 97 296 296 HOH HOH . 
D 4 HOH A 98 297 297 HOH HOH . 
D 4 HOH A 99 298 298 HOH HOH . 
D 4 HOH A 100 299 299 HOH HOH . 
D 4 HOH A 101 300 300 HOH HOH . 
D 4 HOH A 102 301 301 HOH HOH . 
D 4 HOH A 103 302 302 HOH HOH . 
D 4 HOH A 104 303 303 HOH HOH . 
D 4 HOH A 105 304 304 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 . . . C 3 16.634 -11.407 -21.793 1 7.06 ? PA TYD 160 A 1 
HETATM 2 O O1A TYD . . . C 3 16.219 -12.867 -21.8 1 8.11 ? O1A TYD 160 A 1 
HETATM 3 O O2A TYD . . . C 3 16.524 -10.61 -22.998 1 9.67 ? O2A TYD 160 A 1 
HETATM 4 O O3A TYD . . . C 3 15.773 -10.641 -20.67 1 8.77 ? O3A TYD 160 A 1 
HETATM 5 P PB TYD . . . C 3 14.681 -11.094 -19.566 1 6.82 ? PB TYD 160 A 1 
HETATM 6 O O1B TYD . . . C 3 15.443 -11.044 -18.307 1 7.43 ? O1B TYD 160 A 1 
HETATM 7 O O2B TYD . . . C 3 14.287 -12.514 -19.907 1 7.26 ? O2B TYD 160 A 1 
HETATM 8 O O3B TYD . . . C 3 13.62 -10.096 -19.691 1 9.34 ? O3B TYD 160 A 1 
HETATM 9 O O5' TYD . . . C 3 18.138 -11.284 -21.252 1 4.44 ? O5' TYD 160 A 1 
HETATM 10 C C5' TYD . . . C 3 18.457 -11.907 -19.996 1 6.17 ? C5' TYD 160 A 1 
HETATM 11 C C4' TYD . . . C 3 19.207 -10.96 -19.107 1 6.8 ? C4' TYD 160 A 1 
HETATM 12 O O4' TYD . . . C 3 20.35 -10.541 -19.811 1 10.53 ? O4' TYD 160 A 1 
HETATM 13 C C3' TYD . . . C 3 18.49 -9.655 -18.781 1 8.39 ? C3' TYD 160 A 1 
HETATM 14 O O3' TYD . . . C 3 17.656 -10.054 -17.699 1 10.29 ? O3' TYD 160 A 1 
HETATM 15 C C2' TYD . . . C 3 19.648 -8.765 -18.408 1 7.61 ? C2' TYD 160 A 1 
HETATM 16 C C1' TYD . . . C 3 20.741 -9.203 -19.415 1 9.15 ? C1' TYD 160 A 1 
HETATM 17 N N1 TYD . . . C 3 20.795 -8.342 -20.623 1 8.55 ? N1 TYD 160 A 1 
HETATM 18 C C2 TYD . . . C 3 21.603 -7.208 -20.613 1 9.57 ? C2 TYD 160 A 1 
HETATM 19 O O2 TYD . . . C 3 22.324 -6.949 -19.653 1 11.22 ? O2 TYD 160 A 1 
HETATM 20 N N3 TYD . . . C 3 21.573 -6.39 -21.756 1 8.91 ? N3 TYD 160 A 1 
HETATM 21 C C4 TYD . . . C 3 20.81 -6.645 -22.891 1 9.68 ? C4 TYD 160 A 1 
HETATM 22 O O4 TYD . . . C 3 20.879 -5.881 -23.847 1 14.18 ? O4 TYD 160 A 1 
HETATM 23 C C5 TYD . . . C 3 19.985 -7.833 -22.803 1 8.5 ? C5 TYD 160 A 1 
HETATM 24 C C5M TYD . . . C 3 19.146 -8.28 -23.993 1 8.31 ? C5M TYD 160 A 1 
HETATM 25 C C6 TYD . . . C 3 19.961 -8.59 -21.694 1 8.62 ? C6 TYD 160 A 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#