data_4KD4 # _model_server_result.job_id jM9B59O_uLOhLjUsECJZPA _model_server_result.datetime_utc '2024-10-11 10:21:41' _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 4kd4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 4KD4 # _exptl.entry_id 4KD4 _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 4KD4 _cell.length_a 47.64 _cell.length_b 47.64 _cell.length_c 62.806 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KD4 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc4 B CA CA . A CA 201 1_555 C O6P THP . A THP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? metalc ? metalc5 B CA CA . A CA 201 1_555 F O HOH . A HOH 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc6 B CA CA . A CA 201 1_555 F O HOH . A HOH 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? # _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 4KD4 _atom_sites.fract_transf_matrix[1][1] 0.020991 _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] 0.020991 _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] 0.015922 _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 MRD A 1 203 1 MRD MRD . E 5 PO4 A 1 204 1 PO4 PO4 . 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 43 HOH HOH . F 6 HOH A 43 343 44 HOH HOH . F 6 HOH A 44 344 45 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 53 HOH HOH . F 6 HOH A 52 352 54 HOH HOH . F 6 HOH A 53 353 56 HOH HOH . F 6 HOH A 54 354 57 HOH HOH . F 6 HOH A 55 355 59 HOH HOH . F 6 HOH A 56 356 60 HOH HOH . F 6 HOH A 57 357 62 HOH HOH . F 6 HOH A 58 358 63 HOH HOH . F 6 HOH A 59 359 67 HOH HOH . F 6 HOH A 60 360 69 HOH HOH . F 6 HOH A 61 361 70 HOH HOH . F 6 HOH A 62 362 71 HOH HOH . F 6 HOH A 63 363 72 HOH HOH . F 6 HOH A 64 364 73 HOH HOH . F 6 HOH A 65 365 75 HOH HOH . F 6 HOH A 66 366 77 HOH HOH . F 6 HOH A 67 367 78 HOH HOH . F 6 HOH A 68 368 79 HOH HOH . F 6 HOH A 69 369 80 HOH HOH . F 6 HOH A 70 370 81 HOH HOH . F 6 HOH A 71 371 82 HOH HOH . F 6 HOH A 72 372 83 HOH HOH . F 6 HOH A 73 373 84 HOH HOH . F 6 HOH A 74 374 85 HOH HOH . F 6 HOH A 75 375 86 HOH HOH . F 6 HOH A 76 376 87 HOH HOH . F 6 HOH A 77 377 88 HOH HOH . F 6 HOH A 78 378 89 HOH HOH . F 6 HOH A 79 379 90 HOH HOH . F 6 HOH A 80 380 91 HOH HOH . F 6 HOH A 81 381 92 HOH HOH . F 6 HOH A 82 382 93 HOH HOH . F 6 HOH A 83 383 94 HOH HOH . F 6 HOH A 84 384 95 HOH HOH . F 6 HOH A 85 385 96 HOH HOH . F 6 HOH A 86 386 97 HOH HOH . F 6 HOH A 87 387 98 HOH HOH . F 6 HOH A 88 388 99 HOH HOH . F 6 HOH A 89 389 100 HOH HOH . F 6 HOH A 90 390 101 HOH HOH . F 6 HOH A 91 391 102 HOH HOH . F 6 HOH A 92 392 103 HOH HOH . F 6 HOH A 93 393 104 HOH HOH . F 6 HOH A 94 394 105 HOH HOH . F 6 HOH A 95 395 106 HOH HOH . F 6 HOH A 96 396 107 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 -17.49 10.2 -2.971 1 26.57 ? P2 THP 202 A 1 HETATM 2 O O4P THP . . . C 3 -17.044 11.626 -3.504 1 33.38 ? O4P THP 202 A 1 HETATM 3 O O5P THP . . . C 3 -16.327 9.359 -2.564 1 24.36 ? O5P THP 202 A 1 HETATM 4 O O6P THP . . . C 3 -18.626 10.289 -2.092 1 26.33 ? O6P THP 202 A 1 HETATM 5 P P1 THP . . . C 3 -18.912 12.353 -8.809 1 30.43 ? P1 THP 202 A 1 HETATM 6 O O1P THP . . . C 3 -18.626 12.578 -10.303 1 35.66 ? O1P THP 202 A 1 HETATM 7 O O2P THP . . . C 3 -17.695 12.575 -8.017 1 38.94 ? O2P THP 202 A 1 HETATM 8 O O3P THP . . . C 3 -20.106 13.016 -8.243 1 38.42 ? O3P THP 202 A 1 HETATM 9 O O5' THP . . . C 3 -18.121 9.472 -4.262 1 31.48 ? O5' THP 202 A 1 HETATM 10 C C5' THP . . . C 3 -19.198 9.979 -5.048 1 32.36 ? C5' THP 202 A 1 HETATM 11 C C4' THP . . . C 3 -18.722 9.872 -6.497 1 28.61 ? C4' THP 202 A 1 HETATM 12 O O4' THP . . . C 3 -18.445 8.481 -6.794 1 26.65 ? O4' THP 202 A 1 HETATM 13 C C3' THP . . . C 3 -19.868 10.236 -7.441 1 30.83 ? C3' THP 202 A 1 HETATM 14 O O3' THP . . . C 3 -19.298 10.788 -8.662 1 30.84 ? O3' THP 202 A 1 HETATM 15 C C2' THP . . . C 3 -20.54 8.936 -7.778 1 31.1 ? C2' THP 202 A 1 HETATM 16 C C1' THP . . . C 3 -19.336 7.96 -7.734 1 28.99 ? C1' THP 202 A 1 HETATM 17 N N1 THP . . . C 3 -19.801 6.684 -7.285 1 24.85 ? N1 THP 202 A 1 HETATM 18 C C2 THP . . . C 3 -20.199 5.747 -8.214 1 29.08 ? C2 THP 202 A 1 HETATM 19 O O2 THP . . . C 3 -20.061 6.01 -9.471 1 24.68 ? O2 THP 202 A 1 HETATM 20 N N3 THP . . . C 3 -20.67 4.564 -7.869 1 23.39 ? N3 THP 202 A 1 HETATM 21 C C4 THP . . . C 3 -20.891 4.223 -6.548 1 20.6 ? C4 THP 202 A 1 HETATM 22 O O4 THP . . . C 3 -21.496 3.153 -6.284 1 21.34 ? O4 THP 202 A 1 HETATM 23 C C5 THP . . . C 3 -20.49 5.264 -5.624 1 20.43 ? C5 THP 202 A 1 HETATM 24 C C5M THP . . . C 3 -20.587 4.952 -4.104 1 21.95 ? C5M THP 202 A 1 HETATM 25 C C6 THP . . . C 3 -19.937 6.419 -5.93 1 22.35 ? C6 THP 202 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #