data_2OF1
#
_model_server_result.job_id            BwlJIiGe9B0w2TA20-gBKw 
_model_server_result.datetime_utc      '2024-10-11 10:20:12' 
_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          2of1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":501}' 
#
_entry.id    2OF1 
#
_exptl.entry_id    2OF1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-3',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         90 
_cell.entry_id            2OF1 
_cell.length_a            60.313 
_cell.length_b            63.62 
_cell.length_c            46.727 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2OF1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_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 A OD2 ASP 21 A ASP 21 1_555 B CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? 
metalc ? metalc3 F O HOH . A HOH 220 1_555 B CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? 
metalc ? metalc4 E O4P THP . A THP 501 1_555 B CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                THP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-3',5'-DIPHOSPHATE" 
_chem_comp.type              'dna linking' 
_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
P2 O4P THP doub 286 n n 
P2 O5P THP sing 287 n n 
P2 O6P THP sing 288 n n 
P2 O5' THP sing 289 n n 
O5P HOP5 THP sing 290 n n 
O6P HOP6 THP sing 291 n n 
P1 O1P THP doub 292 n n 
P1 O2P THP sing 293 n n 
P1 O3P THP sing 294 n n 
P1 O3' THP sing 295 n n 
O2P HOP2 THP sing 296 n n 
O3P HOP3 THP sing 297 n n 
O5' C5' THP sing 298 n n 
C5' C4' THP sing 299 n n 
C5' "H5'1" THP sing 300 n n 
C5' "H5'2" THP sing 301 n n 
C4' O4' THP sing 302 n n 
C4' C3' THP sing 303 n n 
C4' H4' THP sing 304 n n 
O4' C1' THP sing 305 n n 
C3' O3' THP sing 306 n n 
C3' C2' THP sing 307 n n 
C3' H3' THP sing 308 n n 
C2' C1' THP sing 309 n n 
C2' "H2'1" THP sing 310 n n 
C2' "H2'2" THP sing 311 n n 
C1' N1 THP sing 312 n n 
C1' H1' THP sing 313 n n 
N1 C2 THP sing 314 n n 
N1 C6 THP sing 315 n n 
C2 O2 THP doub 316 n n 
C2 N3 THP sing 317 n n 
N3 C4 THP sing 318 n n 
N3 H3 THP sing 319 n n 
C4 O4 THP doub 320 n n 
C4 C5 THP sing 321 n n 
C5 C5M THP sing 322 n n 
C5 C6 THP doub 323 n n 
C5M H51 THP sing 324 n n 
C5M H52 THP sing 325 n n 
C5M H53 THP sing 326 n n 
C6 H6 THP sing 327 n n 
#
_atom_sites.entry_id                     2OF1 
_atom_sites.fract_transf_matrix[1][1]    0.01658 
_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]    0.015718 
_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]    0.021401 
_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 CA A 1 502 502 CA CA . 
C 3 DMS A 1 402 402 DMS DMS . 
D 3 DMS A 1 403 403 DMS DMS . 
E 4 THP A 1 501 501 THP THP . 
F 5 HOH A 1 201 201 HOH HOH . 
F 5 HOH A 2 202 202 HOH HOH . 
F 5 HOH A 3 203 203 HOH HOH . 
F 5 HOH A 4 204 204 HOH HOH . 
F 5 HOH A 5 205 205 HOH HOH . 
F 5 HOH A 6 206 206 HOH HOH . 
F 5 HOH A 7 207 207 HOH HOH . 
F 5 HOH A 8 208 208 HOH HOH . 
F 5 HOH A 9 209 209 HOH HOH . 
F 5 HOH A 10 210 210 HOH HOH . 
F 5 HOH A 11 211 211 HOH HOH . 
F 5 HOH A 12 212 212 HOH HOH . 
F 5 HOH A 13 213 213 HOH HOH . 
F 5 HOH A 14 214 214 HOH HOH . 
F 5 HOH A 15 215 215 HOH HOH . 
F 5 HOH A 16 216 216 HOH HOH . 
F 5 HOH A 17 217 217 HOH HOH . 
F 5 HOH A 18 218 218 HOH HOH . 
F 5 HOH A 19 219 219 HOH HOH . 
F 5 HOH A 20 220 220 HOH HOH . 
F 5 HOH A 21 221 221 HOH HOH . 
F 5 HOH A 22 222 222 HOH HOH . 
F 5 HOH A 23 223 223 HOH HOH . 
F 5 HOH A 24 224 224 HOH HOH . 
F 5 HOH A 25 225 225 HOH HOH . 
F 5 HOH A 26 226 226 HOH HOH . 
F 5 HOH A 27 227 227 HOH HOH . 
F 5 HOH A 28 228 228 HOH HOH . 
F 5 HOH A 29 229 229 HOH HOH . 
F 5 HOH A 30 230 230 HOH HOH . 
F 5 HOH A 31 231 231 HOH HOH . 
F 5 HOH A 32 232 232 HOH HOH . 
F 5 HOH A 33 233 233 HOH HOH . 
F 5 HOH A 34 234 234 HOH HOH . 
F 5 HOH A 35 235 235 HOH HOH . 
F 5 HOH A 36 236 236 HOH HOH . 
F 5 HOH A 37 237 237 HOH HOH . 
F 5 HOH A 38 238 238 HOH HOH . 
F 5 HOH A 39 239 239 HOH HOH . 
F 5 HOH A 40 240 240 HOH HOH . 
F 5 HOH A 41 241 241 HOH HOH . 
F 5 HOH A 42 242 242 HOH HOH . 
F 5 HOH A 43 243 243 HOH HOH . 
F 5 HOH A 44 244 244 HOH HOH . 
F 5 HOH A 45 245 245 HOH HOH . 
F 5 HOH A 46 246 246 HOH HOH . 
F 5 HOH A 47 247 247 HOH HOH . 
F 5 HOH A 48 248 248 HOH HOH . 
F 5 HOH A 49 249 249 HOH HOH . 
F 5 HOH A 50 250 250 HOH HOH . 
F 5 HOH A 51 251 251 HOH HOH . 
F 5 HOH A 52 252 252 HOH HOH . 
F 5 HOH A 53 253 253 HOH HOH . 
F 5 HOH A 54 254 254 HOH HOH . 
F 5 HOH A 55 255 255 HOH HOH . 
F 5 HOH A 56 256 256 HOH HOH . 
F 5 HOH A 57 257 257 HOH HOH . 
F 5 HOH A 58 258 258 HOH HOH . 
F 5 HOH A 59 259 259 HOH HOH . 
F 5 HOH A 60 260 260 HOH HOH . 
F 5 HOH A 61 261 261 HOH HOH . 
F 5 HOH A 62 262 262 HOH HOH . 
F 5 HOH A 63 263 263 HOH HOH . 
F 5 HOH A 64 264 264 HOH HOH . 
F 5 HOH A 65 265 265 HOH HOH . 
F 5 HOH A 66 266 266 HOH HOH . 
F 5 HOH A 67 267 267 HOH HOH . 
F 5 HOH A 68 268 268 HOH HOH . 
F 5 HOH A 69 269 269 HOH HOH . 
F 5 HOH A 70 270 270 HOH HOH . 
F 5 HOH A 71 271 271 HOH HOH . 
F 5 HOH A 72 272 272 HOH HOH . 
F 5 HOH A 73 273 273 HOH HOH . 
F 5 HOH A 74 274 274 HOH HOH . 
F 5 HOH A 75 275 275 HOH HOH . 
F 5 HOH A 76 276 276 HOH HOH . 
F 5 HOH A 77 277 277 HOH HOH . 
F 5 HOH A 78 278 278 HOH HOH . 
F 5 HOH A 79 279 279 HOH HOH . 
F 5 HOH A 80 280 280 HOH HOH . 
F 5 HOH A 81 281 281 HOH HOH . 
F 5 HOH A 82 282 282 HOH HOH . 
F 5 HOH A 83 283 283 HOH HOH . 
F 5 HOH A 84 284 284 HOH HOH . 
F 5 HOH A 85 285 285 HOH HOH . 
F 5 HOH A 86 286 286 HOH HOH . 
F 5 HOH A 87 287 287 HOH HOH . 
F 5 HOH A 88 288 288 HOH HOH . 
F 5 HOH A 89 289 289 HOH HOH . 
F 5 HOH A 90 290 290 HOH HOH . 
F 5 HOH A 91 291 291 HOH HOH . 
F 5 HOH A 92 292 292 HOH HOH . 
F 5 HOH A 93 293 293 HOH HOH . 
F 5 HOH A 94 294 294 HOH HOH . 
F 5 HOH A 95 295 295 HOH HOH . 
F 5 HOH A 96 296 296 HOH HOH . 
F 5 HOH A 97 297 297 HOH HOH . 
F 5 HOH A 98 298 298 HOH HOH . 
F 5 HOH A 99 299 299 HOH HOH . 
F 5 HOH A 100 300 300 HOH HOH . 
F 5 HOH A 101 301 301 HOH HOH . 
F 5 HOH A 102 302 302 HOH HOH . 
F 5 HOH A 103 303 303 HOH HOH . 
F 5 HOH A 104 304 304 HOH HOH . 
F 5 HOH A 105 305 305 HOH HOH . 
F 5 HOH A 106 306 306 HOH HOH . 
F 5 HOH A 107 307 307 HOH HOH . 
F 5 HOH A 108 308 308 HOH HOH . 
F 5 HOH A 109 309 309 HOH HOH . 
F 5 HOH A 110 310 310 HOH HOH . 
F 5 HOH A 111 311 311 HOH HOH . 
F 5 HOH A 112 312 312 HOH HOH . 
F 5 HOH A 113 313 313 HOH HOH . 
F 5 HOH A 114 314 314 HOH HOH . 
F 5 HOH A 115 315 315 HOH HOH . 
F 5 HOH A 116 316 316 HOH HOH . 
F 5 HOH A 117 317 317 HOH HOH . 
F 5 HOH A 118 318 318 HOH HOH . 
F 5 HOH A 119 319 319 HOH HOH . 
F 5 HOH A 120 320 320 HOH HOH . 
F 5 HOH A 121 321 321 HOH HOH . 
F 5 HOH A 122 322 322 HOH HOH . 
F 5 HOH A 123 323 323 HOH HOH . 
F 5 HOH A 124 324 324 HOH HOH . 
F 5 HOH A 125 325 325 HOH HOH . 
F 5 HOH A 126 326 326 HOH HOH . 
F 5 HOH A 127 327 327 HOH HOH . 
F 5 HOH A 128 328 328 HOH HOH . 
F 5 HOH A 129 329 329 HOH HOH . 
F 5 HOH A 130 330 330 HOH HOH . 
F 5 HOH A 131 331 331 HOH HOH . 
F 5 HOH A 132 332 332 HOH HOH . 
F 5 HOH A 133 333 333 HOH HOH . 
F 5 HOH A 134 334 334 HOH HOH . 
F 5 HOH A 135 335 335 HOH HOH . 
F 5 HOH A 136 336 336 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 P2 THP . . . E 4 47.89 53.14 20.745 1 25.37 ? P2 THP 501 A 1 
HETATM 2 O O4P THP . . . E 4 48.76 52.642 19.657 1 23.52 ? O4P THP 501 A 1 
HETATM 3 O O5P THP . . . E 4 46.451 53.342 20.536 1 22.44 ? O5P THP 501 A 1 
HETATM 4 O O6P THP . . . E 4 48.511 54.489 21.305 1 26.09 ? O6P THP 501 A 1 
HETATM 5 P P1 THP . . . E 4 52.107 52.12 26.32 1 25.94 ? P1 THP 501 A 1 
HETATM 6 O O1P THP . . . E 4 52.674 52.914 25.236 1 26.19 ? O1P THP 501 A 1 
HETATM 7 O O2P THP . . . E 4 52.623 50.865 26.873 1 28.18 ? O2P THP 501 A 1 
HETATM 8 O O3P THP . . . E 4 51.919 53.099 27.556 1 28.06 ? O3P THP 501 A 1 
HETATM 9 O O5' THP . . . E 4 48.037 52.165 21.972 1 20.08 ? O5' THP 501 A 1 
HETATM 10 C C5' THP . . . E 4 49.276 51.728 22.454 1 21.85 ? C5' THP 501 A 1 
HETATM 11 C C4' THP . . . E 4 49.122 51.586 23.946 1 21.18 ? C4' THP 501 A 1 
HETATM 12 O O4' THP . . . E 4 48.079 50.667 24.24 1 20.26 ? O4' THP 501 A 1 
HETATM 13 C C3' THP . . . E 4 50.381 51.065 24.568 1 21.76 ? C3' THP 501 A 1 
HETATM 14 O O3' THP . . . E 4 50.63 51.802 25.764 1 25.59 ? O3' THP 501 A 1 
HETATM 15 C C2' THP . . . E 4 50.122 49.613 24.861 1 21.06 ? C2' THP 501 A 1 
HETATM 16 C C1' THP . . . E 4 48.585 49.57 24.977 1 20.08 ? C1' THP 501 A 1 
HETATM 17 N N1 THP . . . E 4 48.144 48.288 24.39 1 21.08 ? N1 THP 501 A 1 
HETATM 18 C C2 THP . . . E 4 48.107 47.173 25.218 1 22.59 ? C2 THP 501 A 1 
HETATM 19 O O2 THP . . . E 4 48.412 47.189 26.401 1 24.85 ? O2 THP 501 A 1 
HETATM 20 N N3 THP . . . E 4 47.704 45.997 24.645 1 22.3 ? N3 THP 501 A 1 
HETATM 21 C C4 THP . . . E 4 47.331 45.832 23.322 1 20.9 ? C4 THP 501 A 1 
HETATM 22 O O4 THP . . . E 4 46.998 44.721 22.951 1 19.05 ? O4 THP 501 A 1 
HETATM 23 C C5 THP . . . E 4 47.377 47.026 22.499 1 20.56 ? C5 THP 501 A 1 
HETATM 24 C C5M THP . . . E 4 46.975 46.945 21.007 1 18.4 ? C5M THP 501 A 1 
HETATM 25 C C6 THP . . . E 4 47.777 48.197 23.048 1 20.01 ? C6 THP 501 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           25 
#