data_4QF4 # _model_server_result.job_id uF5lTjKLnn-6vQaOCi6sAw _model_server_result.datetime_utc '2024-11-26 01:13:39' _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 4qf4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 4QF4 # _exptl.entry_id 4QF4 _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-3',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 4QF4 _cell.length_a 67.53 _cell.length_b 67.53 _cell.length_c 62.817 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QF4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 B,F,G,H,J 2 1 A,C,D,E,I 3 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 F N 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 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc4 C O4P THP . A THP 201 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.81 ? metalc ? metalc5 D CA CA . A CA 202 1_555 I O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc6 D CA CA . A CA 202 1_555 I O HOH . A HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc7 D CA CA . A CA 202 1_555 I O HOH . A HOH 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc8 B OD1 ASP 21 B ASP 21 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc9 B OD1 ASP 40 B ASP 40 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc10 B O THR 41 B THR 41 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc11 F O4P THP . B THP 201 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc12 G CA CA . B CA 202 1_555 J O HOH . B HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc13 G CA CA . B CA 202 1_555 J O HOH . B HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc14 G CA CA . B CA 202 1_555 J O HOH . B HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? # _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 281 n n P2 O5P THP sing 282 n n P2 O6P THP sing 283 n n P2 O5' THP sing 284 n n O5P HOP5 THP sing 285 n n O6P HOP6 THP sing 286 n n P1 O1P THP doub 287 n n P1 O2P THP sing 288 n n P1 O3P THP sing 289 n n P1 O3' THP sing 290 n n O2P HOP2 THP sing 291 n n O3P HOP3 THP sing 292 n n O5' C5' THP sing 293 n n C5' C4' THP sing 294 n n C5' "H5'1" THP sing 295 n n C5' "H5'2" THP sing 296 n n C4' O4' THP sing 297 n n C4' C3' THP sing 298 n n C4' H4' THP sing 299 n n O4' C1' THP sing 300 n n C3' O3' THP sing 301 n n C3' C2' THP sing 302 n n C3' H3' THP sing 303 n n C2' C1' THP sing 304 n n C2' "H2'1" THP sing 305 n n C2' "H2'2" THP sing 306 n n C1' N1 THP sing 307 n n C1' H1' THP sing 308 n n N1 C2 THP sing 309 n n N1 C6 THP sing 310 n n C2 O2 THP doub 311 n n C2 N3 THP sing 312 n n N3 C4 THP sing 313 n n N3 H3 THP sing 314 n n C4 O4 THP doub 315 n n C4 C5 THP sing 316 n n C5 C5M THP sing 317 n n C5 C6 THP doub 318 n n C5M H51 THP sing 319 n n C5M H52 THP sing 320 n n C5M H53 THP sing 321 n n C6 H6 THP sing 322 n n # _atom_sites.entry_id 4QF4 _atom_sites.fract_transf_matrix[1][1] 0.014808 _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] 0.014808 _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] 0.015919 _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 THP A 1 201 1 THP THP . D 3 CA A 1 202 1 CA CA . E 4 PO4 A 1 203 2 PO4 PO4 . F 2 THP B 1 201 1 THP THP . G 3 CA B 1 202 1 CA CA . H 4 PO4 B 1 203 1 PO4 PO4 . I 5 HOH A 1 301 1 HOH HOH . I 5 HOH A 2 302 2 HOH HOH . I 5 HOH A 3 303 4 HOH HOH . I 5 HOH A 4 304 7 HOH HOH . I 5 HOH A 5 305 12 HOH HOH . I 5 HOH A 6 306 13 HOH HOH . I 5 HOH A 7 307 15 HOH HOH . I 5 HOH A 8 308 17 HOH HOH . I 5 HOH A 9 309 18 HOH HOH . I 5 HOH A 10 310 19 HOH HOH . I 5 HOH A 11 311 20 HOH HOH . I 5 HOH A 12 312 25 HOH HOH . I 5 HOH A 13 313 27 HOH HOH . I 5 HOH A 14 314 30 HOH HOH . I 5 HOH A 15 315 31 HOH HOH . I 5 HOH A 16 316 36 HOH HOH . I 5 HOH A 17 317 37 HOH HOH . I 5 HOH A 18 318 41 HOH HOH . I 5 HOH A 19 319 44 HOH HOH . I 5 HOH A 20 320 46 HOH HOH . I 5 HOH A 21 321 47 HOH HOH . I 5 HOH A 22 322 48 HOH HOH . I 5 HOH A 23 323 49 HOH HOH . I 5 HOH A 24 324 50 HOH HOH . I 5 HOH A 25 325 51 HOH HOH . I 5 HOH A 26 326 52 HOH HOH . I 5 HOH A 27 327 59 HOH HOH . I 5 HOH A 28 328 60 HOH HOH . I 5 HOH A 29 329 61 HOH HOH . I 5 HOH A 30 330 62 HOH HOH . I 5 HOH A 31 331 63 HOH HOH . I 5 HOH A 32 332 64 HOH HOH . I 5 HOH A 33 333 66 HOH HOH . I 5 HOH A 34 334 67 HOH HOH . I 5 HOH A 35 335 68 HOH HOH . I 5 HOH A 36 336 69 HOH HOH . I 5 HOH A 37 337 70 HOH HOH . I 5 HOH A 38 338 81 HOH HOH . I 5 HOH A 39 339 82 HOH HOH . I 5 HOH A 40 340 83 HOH HOH . I 5 HOH A 41 341 84 HOH HOH . I 5 HOH A 42 342 85 HOH HOH . I 5 HOH A 43 343 86 HOH HOH . I 5 HOH A 44 344 93 HOH HOH . I 5 HOH A 45 345 95 HOH HOH . I 5 HOH A 46 346 96 HOH HOH . I 5 HOH A 47 347 105 HOH HOH . I 5 HOH A 48 348 106 HOH HOH . I 5 HOH A 49 349 108 HOH HOH . I 5 HOH A 50 350 109 HOH HOH . I 5 HOH A 51 351 110 HOH HOH . I 5 HOH A 52 352 113 HOH HOH . I 5 HOH A 53 353 114 HOH HOH . J 5 HOH B 1 301 3 HOH HOH . J 5 HOH B 2 302 5 HOH HOH . J 5 HOH B 3 303 6 HOH HOH . J 5 HOH B 4 304 8 HOH HOH . J 5 HOH B 5 305 9 HOH HOH . J 5 HOH B 6 306 10 HOH HOH . J 5 HOH B 7 307 11 HOH HOH . J 5 HOH B 8 308 14 HOH HOH . J 5 HOH B 9 309 16 HOH HOH . J 5 HOH B 10 310 21 HOH HOH . J 5 HOH B 11 311 22 HOH HOH . J 5 HOH B 12 312 23 HOH HOH . J 5 HOH B 13 313 24 HOH HOH . J 5 HOH B 14 314 28 HOH HOH . J 5 HOH B 15 315 29 HOH HOH . J 5 HOH B 16 316 32 HOH HOH . J 5 HOH B 17 317 33 HOH HOH . J 5 HOH B 18 318 34 HOH HOH . J 5 HOH B 19 319 35 HOH HOH . J 5 HOH B 20 320 38 HOH HOH . J 5 HOH B 21 321 39 HOH HOH . J 5 HOH B 22 322 40 HOH HOH . J 5 HOH B 23 323 42 HOH HOH . J 5 HOH B 24 324 43 HOH HOH . J 5 HOH B 25 325 45 HOH HOH . J 5 HOH B 26 326 53 HOH HOH . J 5 HOH B 27 327 54 HOH HOH . J 5 HOH B 28 328 55 HOH HOH . J 5 HOH B 29 329 56 HOH HOH . J 5 HOH B 30 330 57 HOH HOH . J 5 HOH B 31 331 58 HOH HOH . J 5 HOH B 32 332 71 HOH HOH . J 5 HOH B 33 333 72 HOH HOH . J 5 HOH B 34 334 73 HOH HOH . J 5 HOH B 35 335 74 HOH HOH . J 5 HOH B 36 336 75 HOH HOH . J 5 HOH B 37 337 76 HOH HOH . J 5 HOH B 38 338 77 HOH HOH . J 5 HOH B 39 339 78 HOH HOH . J 5 HOH B 40 340 79 HOH HOH . J 5 HOH B 41 341 80 HOH HOH . J 5 HOH B 42 342 87 HOH HOH . J 5 HOH B 43 343 88 HOH HOH . J 5 HOH B 44 344 89 HOH HOH . J 5 HOH B 45 345 90 HOH HOH . J 5 HOH B 46 346 91 HOH HOH . J 5 HOH B 47 347 92 HOH HOH . J 5 HOH B 48 348 94 HOH HOH . J 5 HOH B 49 349 97 HOH HOH . J 5 HOH B 50 350 98 HOH HOH . J 5 HOH B 51 351 99 HOH HOH . J 5 HOH B 52 352 100 HOH HOH . J 5 HOH B 53 353 101 HOH HOH . J 5 HOH B 54 354 102 HOH HOH . J 5 HOH B 55 355 103 HOH HOH . J 5 HOH B 56 356 104 HOH HOH . J 5 HOH B 57 357 107 HOH HOH . J 5 HOH B 58 358 111 HOH HOH . J 5 HOH B 59 359 112 HOH HOH . J 5 HOH B 60 360 115 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 . . . F 2 28.576 13.945 -12.919 1 37.59 ? P2 THP 201 B 1 HETATM 2 O O4P THP . . . F 2 27.904 13.195 -14.03 1 33.99 ? O4P THP 201 B 1 HETATM 3 O O5P THP . . . F 2 29.024 15.37 -13.246 1 30.43 ? O5P THP 201 B 1 HETATM 4 O O6P THP . . . F 2 29.651 13.055 -12.298 1 35.79 ? O6P THP 201 B 1 HETATM 5 P P1 THP . . . F 2 29.058 11.519 -7.021 1 39.96 ? P1 THP 201 B 1 HETATM 6 O O1P THP . . . F 2 28.455 10.154 -7.217 1 45.17 ? O1P THP 201 B 1 HETATM 7 O O2P THP . . . F 2 30.105 12.013 -7.94 1 35.98 ? O2P THP 201 B 1 HETATM 8 O O3P THP . . . F 2 29.492 11.801 -5.58 1 43.34 ? O3P THP 201 B 1 HETATM 9 O O5' THP . . . F 2 27.535 14.077 -11.712 1 34.97 ? O5' THP 201 B 1 HETATM 10 C C5' THP . . . F 2 27.164 13.016 -10.865 1 35.65 ? C5' THP 201 B 1 HETATM 11 C C4' THP . . . F 2 27.544 13.416 -9.437 1 37.15 ? C4' THP 201 B 1 HETATM 12 O O4' THP . . . F 2 26.846 14.659 -9.122 1 35.4 ? O4' THP 201 B 1 HETATM 13 C C3' THP . . . F 2 26.999 12.364 -8.499 1 37.11 ? C3' THP 201 B 1 HETATM 14 O O3' THP . . . F 2 27.756 12.441 -7.271 1 41.5 ? O3' THP 201 B 1 HETATM 15 C C2' THP . . . F 2 25.599 12.828 -8.18 1 39.66 ? C2' THP 201 B 1 HETATM 16 C C1' THP . . . F 2 25.751 14.368 -8.255 1 34.96 ? C1' THP 201 B 1 HETATM 17 N N1 THP . . . F 2 24.488 14.899 -8.662 1 32.95 ? N1 THP 201 B 1 HETATM 18 C C2 THP . . . F 2 23.557 15.278 -7.659 1 35.7 ? C2 THP 201 B 1 HETATM 19 O O2 THP . . . F 2 23.863 15.21 -6.419 1 33.51 ? O2 THP 201 B 1 HETATM 20 N N3 THP . . . F 2 22.33 15.67 -7.994 1 31.54 ? N3 THP 201 B 1 HETATM 21 C C4 THP . . . F 2 21.994 15.791 -9.308 1 29.74 ? C4 THP 201 B 1 HETATM 22 O O4 THP . . . F 2 20.855 16.167 -9.505 1 26.07 ? O4 THP 201 B 1 HETATM 23 C C5 THP . . . F 2 22.937 15.384 -10.368 1 28.98 ? C5 THP 201 B 1 HETATM 24 C C5M THP . . . F 2 22.619 15.411 -11.9 1 26.97 ? C5M THP 201 B 1 HETATM 25 C C6 THP . . . F 2 24.179 14.938 -9.988 1 33.29 ? C6 THP 201 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #