data_4K5W # _model_server_result.job_id qprVz_WDJ0vmmyMR-8ygCA _model_server_result.datetime_utc '2024-10-20 03:35:59' _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 4k5w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 4K5W # _exptl.entry_id 4K5W _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-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 4K5W _cell.length_a 47.641 _cell.length_b 47.641 _cell.length_c 62.658 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K5W _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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 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 A OD1 ASP 21 A ASP 21 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc4 B CA CA . A CA 201 1_555 C O6P THP . A THP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc5 B CA CA . A CA 201 1_555 F O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc6 B CA CA . A CA 201 1_555 F O HOH . A HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc7 B CA CA . A CA 201 1_555 F O HOH . A HOH 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? # _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 302 n n P2 O5P THP sing 303 n n P2 O6P THP sing 304 n n P2 O5' THP sing 305 n n O5P HOP5 THP sing 306 n n O6P HOP6 THP sing 307 n n P1 O1P THP doub 308 n n P1 O2P THP sing 309 n n P1 O3P THP sing 310 n n P1 O3' THP sing 311 n n O2P HOP2 THP sing 312 n n O3P HOP3 THP sing 313 n n O5' C5' THP sing 314 n n C5' C4' THP sing 315 n n C5' "H5'1" THP sing 316 n n C5' "H5'2" THP sing 317 n n C4' O4' THP sing 318 n n C4' C3' THP sing 319 n n C4' H4' THP sing 320 n n O4' C1' THP sing 321 n n C3' O3' THP sing 322 n n C3' C2' THP sing 323 n n C3' H3' THP sing 324 n n C2' C1' THP sing 325 n n C2' "H2'1" THP sing 326 n n C2' "H2'2" THP sing 327 n n C1' N1 THP sing 328 n n C1' H1' THP sing 329 n n N1 C2 THP sing 330 n n N1 C6 THP sing 331 n n C2 O2 THP doub 332 n n C2 N3 THP sing 333 n n N3 C4 THP sing 334 n n N3 H3 THP sing 335 n n C4 O4 THP doub 336 n n C4 C5 THP sing 337 n n C5 C5M THP sing 338 n n C5 C6 THP doub 339 n n C5M H51 THP sing 340 n n C5M H52 THP sing 341 n n C5M H53 THP sing 342 n n C6 H6 THP sing 343 n n # _atom_sites.entry_id 4K5W _atom_sites.fract_transf_matrix[1][1] 0.02099 _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] 0.02099 _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] 0.01596 _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 1 201 1 CA CA . C 3 THP A 1 202 1 THP THP . D 4 PO4 A 1 203 1 PO4 PO4 . E 5 MRD A 1 204 1 MRD MRD . F 6 HOH A 1 301 1 HOH HOH . F 6 HOH A 2 302 2 HOH HOH . F 6 HOH A 3 303 3 HOH HOH . F 6 HOH A 4 304 4 HOH HOH . F 6 HOH A 5 305 5 HOH HOH . F 6 HOH A 6 306 6 HOH HOH . F 6 HOH A 7 307 7 HOH HOH . F 6 HOH A 8 308 8 HOH HOH . F 6 HOH A 9 309 9 HOH HOH . F 6 HOH A 10 310 10 HOH HOH . F 6 HOH A 11 311 11 HOH HOH . F 6 HOH A 12 312 12 HOH HOH . F 6 HOH A 13 313 13 HOH HOH . F 6 HOH A 14 314 14 HOH HOH . F 6 HOH A 15 315 15 HOH HOH . F 6 HOH A 16 316 16 HOH HOH . F 6 HOH A 17 317 17 HOH HOH . F 6 HOH A 18 318 18 HOH HOH . F 6 HOH A 19 319 19 HOH HOH . F 6 HOH A 20 320 20 HOH HOH . F 6 HOH A 21 321 21 HOH HOH . F 6 HOH A 22 322 22 HOH HOH . F 6 HOH A 23 323 23 HOH HOH . F 6 HOH A 24 324 24 HOH HOH . F 6 HOH A 25 325 25 HOH HOH . F 6 HOH A 26 326 26 HOH HOH . F 6 HOH A 27 327 27 HOH HOH . F 6 HOH A 28 328 28 HOH HOH . F 6 HOH A 29 329 29 HOH HOH . F 6 HOH A 30 330 30 HOH HOH . F 6 HOH A 31 331 31 HOH HOH . F 6 HOH A 32 332 32 HOH HOH . F 6 HOH A 33 333 33 HOH HOH . F 6 HOH A 34 334 34 HOH HOH . F 6 HOH A 35 335 35 HOH HOH . F 6 HOH A 36 336 36 HOH HOH . F 6 HOH A 37 337 37 HOH HOH . F 6 HOH A 38 338 38 HOH HOH . F 6 HOH A 39 339 39 HOH HOH . F 6 HOH A 40 340 40 HOH HOH . F 6 HOH A 41 341 41 HOH HOH . F 6 HOH A 42 342 42 HOH HOH . F 6 HOH A 43 343 43 HOH HOH . F 6 HOH A 44 344 44 HOH HOH . F 6 HOH A 45 345 46 HOH HOH . F 6 HOH A 46 346 47 HOH HOH . F 6 HOH A 47 347 48 HOH HOH . F 6 HOH A 48 348 49 HOH HOH . F 6 HOH A 49 349 50 HOH HOH . F 6 HOH A 50 350 51 HOH HOH . F 6 HOH A 51 351 52 HOH HOH . F 6 HOH A 52 352 53 HOH HOH . F 6 HOH A 53 353 54 HOH HOH . F 6 HOH A 54 354 55 HOH HOH . F 6 HOH A 55 355 56 HOH HOH . F 6 HOH A 56 356 57 HOH HOH . F 6 HOH A 57 357 58 HOH HOH . F 6 HOH A 58 358 59 HOH HOH . F 6 HOH A 59 359 60 HOH HOH . F 6 HOH A 60 360 61 HOH HOH . F 6 HOH A 61 361 62 HOH HOH . F 6 HOH A 62 362 63 HOH HOH . F 6 HOH A 63 363 65 HOH HOH . F 6 HOH A 64 364 66 HOH HOH . F 6 HOH A 65 365 68 HOH HOH . F 6 HOH A 66 366 69 HOH HOH . F 6 HOH A 67 367 70 HOH HOH . F 6 HOH A 68 368 72 HOH HOH . F 6 HOH A 69 369 73 HOH HOH . F 6 HOH A 70 370 74 HOH HOH . F 6 HOH A 71 371 75 HOH HOH . F 6 HOH A 72 372 77 HOH HOH . F 6 HOH A 73 373 79 HOH HOH . F 6 HOH A 74 374 80 HOH HOH . F 6 HOH A 75 375 81 HOH HOH . F 6 HOH A 76 376 82 HOH HOH . F 6 HOH A 77 377 83 HOH HOH . F 6 HOH A 78 378 84 HOH HOH . F 6 HOH A 79 379 86 HOH HOH . F 6 HOH A 80 380 87 HOH HOH . F 6 HOH A 81 381 88 HOH HOH . F 6 HOH A 82 382 89 HOH HOH . F 6 HOH A 83 383 90 HOH HOH . F 6 HOH A 84 384 91 HOH HOH . F 6 HOH A 85 385 93 HOH HOH . F 6 HOH A 86 386 94 HOH HOH . F 6 HOH A 87 387 95 HOH HOH . F 6 HOH A 88 388 96 HOH HOH . F 6 HOH A 89 389 97 HOH HOH . F 6 HOH A 90 390 99 HOH HOH . F 6 HOH A 91 391 100 HOH HOH . F 6 HOH A 92 392 101 HOH HOH . F 6 HOH A 93 393 102 HOH HOH . F 6 HOH A 94 394 103 HOH HOH . F 6 HOH A 95 395 104 HOH HOH . F 6 HOH A 96 396 105 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 . . . C 3 -17.45 10.149 -2.943 1 29.46 ? P2 THP 202 A 1 HETATM 2 O O4P THP . . . C 3 -16.952 11.539 -3.424 1 39.73 ? O4P THP 202 A 1 HETATM 3 O O5P THP . . . C 3 -16.228 9.375 -2.525 1 24.28 ? O5P THP 202 A 1 HETATM 4 O O6P THP . . . C 3 -18.655 10.312 -2.048 1 30.9 ? O6P THP 202 A 1 HETATM 5 P P1 THP . . . C 3 -18.818 12.325 -8.754 1 35.84 ? P1 THP 202 A 1 HETATM 6 O O1P THP . . . C 3 -18.51 12.429 -10.25 1 42.53 ? O1P THP 202 A 1 HETATM 7 O O2P THP . . . C 3 -17.609 12.611 -7.945 1 36.05 ? O2P THP 202 A 1 HETATM 8 O O3P THP . . . C 3 -20.035 13.015 -8.266 1 41.22 ? O3P THP 202 A 1 HETATM 9 O O5' THP . . . C 3 -18.058 9.432 -4.232 1 33 ? O5' THP 202 A 1 HETATM 10 C C5' THP . . . C 3 -19.163 9.904 -4.989 1 33.32 ? C5' THP 202 A 1 HETATM 11 C C4' THP . . . C 3 -18.66 9.86 -6.444 1 31.12 ? C4' THP 202 A 1 HETATM 12 O O4' THP . . . C 3 -18.334 8.497 -6.779 1 30.54 ? O4' THP 202 A 1 HETATM 13 C C3' THP . . . C 3 -19.781 10.238 -7.37 1 32.64 ? C3' THP 202 A 1 HETATM 14 O O3' THP . . . C 3 -19.126 10.735 -8.559 1 35.44 ? O3' THP 202 A 1 HETATM 15 C C2' THP . . . C 3 -20.465 8.944 -7.711 1 34.16 ? C2' THP 202 A 1 HETATM 16 C C1' THP . . . C 3 -19.275 7.979 -7.696 1 32 ? C1' THP 202 A 1 HETATM 17 N N1 THP . . . C 3 -19.785 6.714 -7.271 1 28.38 ? N1 THP 202 A 1 HETATM 18 C C2 THP . . . C 3 -20.183 5.75 -8.227 1 29.95 ? C2 THP 202 A 1 HETATM 19 O O2 THP . . . C 3 -20.067 5.997 -9.488 1 27.98 ? O2 THP 202 A 1 HETATM 20 N N3 THP . . . C 3 -20.685 4.544 -7.9 1 27.47 ? N3 THP 202 A 1 HETATM 21 C C4 THP . . . C 3 -20.885 4.279 -6.561 1 25.79 ? C4 THP 202 A 1 HETATM 22 O O4 THP . . . C 3 -21.437 3.218 -6.312 1 23.1 ? O4 THP 202 A 1 HETATM 23 C C5 THP . . . C 3 -20.47 5.258 -5.576 1 24.66 ? C5 THP 202 A 1 HETATM 24 C C5M THP . . . C 3 -20.644 4.943 -4.052 1 22.49 ? C5M THP 202 A 1 HETATM 25 C C6 THP . . . C 3 -19.897 6.461 -5.922 1 27.04 ? C6 THP 202 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #