data_5CV5 # _model_server_result.job_id P5S9soELKYMmsyTqYIKsRQ _model_server_result.datetime_utc '2024-10-20 03:53:01' _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 5cv5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 5CV5 # _exptl.entry_id 5CV5 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.15 _cell.angle_gamma 90 _cell.entry_id 5CV5 _cell.length_a 30.831 _cell.length_b 60.549 _cell.length_c 77.901 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CV5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 3 D N N ? 3 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 OD2 ASP 21 A ASP 21 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.143 ? metalc ? metalc5 C CA CA . A CA 201 1_555 D O5P THP . A THP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.058 ? metalc ? metalc6 C CA CA . A CA 201 1_555 G O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? metalc ? metalc7 C CA CA . A CA 201 1_555 G O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc8 B OD2 ASP 21 B ASP 21 1_555 E CA CA . B CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? metalc ? metalc9 B OD1 ASP 40 B ASP 40 1_555 E CA CA . B CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc10 B O THR 41 B THR 41 1_555 E CA CA . B CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc11 B OE2 GLU 43 B GLU 43 1_555 E CA CA . B CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc12 E CA CA . B CA 201 1_555 F O4P THP . B THP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.082 ? metalc ? metalc13 E CA CA . B CA 201 1_555 H O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc14 E CA CA . B CA 201 1_555 H O HOH . B HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? # _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 277 n n P2 O5P THP sing 278 n n P2 O6P THP sing 279 n n P2 O5' THP sing 280 n n O5P HOP5 THP sing 281 n n O6P HOP6 THP sing 282 n n P1 O1P THP doub 283 n n P1 O2P THP sing 284 n n P1 O3P THP sing 285 n n P1 O3' THP sing 286 n n O2P HOP2 THP sing 287 n n O3P HOP3 THP sing 288 n n O5' C5' THP sing 289 n n C5' C4' THP sing 290 n n C5' "H5'1" THP sing 291 n n C5' "H5'2" THP sing 292 n n C4' O4' THP sing 293 n n C4' C3' THP sing 294 n n C4' H4' THP sing 295 n n O4' C1' THP sing 296 n n C3' O3' THP sing 297 n n C3' C2' THP sing 298 n n C3' H3' THP sing 299 n n C2' C1' THP sing 300 n n C2' "H2'1" THP sing 301 n n C2' "H2'2" THP sing 302 n n C1' N1 THP sing 303 n n C1' H1' THP sing 304 n n N1 C2 THP sing 305 n n N1 C6 THP sing 306 n n C2 O2 THP doub 307 n n C2 N3 THP sing 308 n n N3 C4 THP sing 309 n n N3 H3 THP sing 310 n n C4 O4 THP doub 311 n n C4 C5 THP sing 312 n n C5 C5M THP sing 313 n n C5 C6 THP doub 314 n n C5M H51 THP sing 315 n n C5M H52 THP sing 316 n n C5M H53 THP sing 317 n n C6 H6 THP sing 318 n n # _atom_sites.entry_id 5CV5 _atom_sites.fract_transf_matrix[1][1] 0.032435 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001787 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016516 _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] 0.012856 _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 CA A 1 201 2 CA CA . D 3 THP A 1 202 143 THP THP . E 2 CA B 1 201 1 CA CA . F 3 THP B 1 202 142 THP THP . G 4 HOH A 1 301 117 HOH HOH . G 4 HOH A 2 302 115 HOH HOH . G 4 HOH A 3 303 28 HOH HOH . G 4 HOH A 4 304 103 HOH HOH . G 4 HOH A 5 305 155 HOH HOH . G 4 HOH A 6 306 3 HOH HOH . G 4 HOH A 7 307 70 HOH HOH . G 4 HOH A 8 308 98 HOH HOH . G 4 HOH A 9 309 106 HOH HOH . G 4 HOH A 10 310 118 HOH HOH . G 4 HOH A 11 311 93 HOH HOH . G 4 HOH A 12 312 1 HOH HOH . G 4 HOH A 13 313 102 HOH HOH . G 4 HOH A 14 314 8 HOH HOH . G 4 HOH A 15 315 68 HOH HOH . G 4 HOH A 16 316 20 HOH HOH . G 4 HOH A 17 317 144 HOH HOH . G 4 HOH A 18 318 40 HOH HOH . G 4 HOH A 19 319 139 HOH HOH . G 4 HOH A 20 320 108 HOH HOH . G 4 HOH A 21 321 9 HOH HOH . G 4 HOH A 22 322 142 HOH HOH . G 4 HOH A 23 323 18 HOH HOH . G 4 HOH A 24 324 16 HOH HOH . G 4 HOH A 25 325 42 HOH HOH . G 4 HOH A 26 326 105 HOH HOH . G 4 HOH A 27 327 23 HOH HOH . G 4 HOH A 28 328 146 HOH HOH . G 4 HOH A 29 329 120 HOH HOH . G 4 HOH A 30 330 109 HOH HOH . G 4 HOH A 31 331 6 HOH HOH . G 4 HOH A 32 332 59 HOH HOH . G 4 HOH A 33 333 15 HOH HOH . G 4 HOH A 34 334 24 HOH HOH . G 4 HOH A 35 335 62 HOH HOH . G 4 HOH A 36 336 140 HOH HOH . G 4 HOH A 37 337 58 HOH HOH . G 4 HOH A 38 338 64 HOH HOH . G 4 HOH A 39 339 44 HOH HOH . G 4 HOH A 40 340 119 HOH HOH . G 4 HOH A 41 341 107 HOH HOH . G 4 HOH A 42 342 56 HOH HOH . G 4 HOH A 43 343 112 HOH HOH . G 4 HOH A 44 344 95 HOH HOH . G 4 HOH A 45 345 27 HOH HOH . G 4 HOH A 46 346 52 HOH HOH . G 4 HOH A 47 347 43 HOH HOH . G 4 HOH A 48 348 96 HOH HOH . G 4 HOH A 49 349 99 HOH HOH . G 4 HOH A 50 350 31 HOH HOH . G 4 HOH A 51 351 51 HOH HOH . G 4 HOH A 52 352 154 HOH HOH . G 4 HOH A 53 353 10 HOH HOH . G 4 HOH A 54 354 60 HOH HOH . G 4 HOH A 55 355 5 HOH HOH . G 4 HOH A 56 356 33 HOH HOH . G 4 HOH A 57 357 53 HOH HOH . G 4 HOH A 58 358 111 HOH HOH . G 4 HOH A 59 359 21 HOH HOH . G 4 HOH A 60 360 94 HOH HOH . G 4 HOH A 61 361 113 HOH HOH . G 4 HOH A 62 362 141 HOH HOH . G 4 HOH A 63 363 47 HOH HOH . G 4 HOH A 64 364 110 HOH HOH . G 4 HOH A 65 365 116 HOH HOH . G 4 HOH A 66 366 57 HOH HOH . G 4 HOH A 67 367 61 HOH HOH . G 4 HOH A 68 368 14 HOH HOH . G 4 HOH A 69 369 121 HOH HOH . G 4 HOH A 70 370 12 HOH HOH . G 4 HOH A 71 371 67 HOH HOH . G 4 HOH A 72 372 101 HOH HOH . G 4 HOH A 73 373 50 HOH HOH . G 4 HOH A 74 374 13 HOH HOH . G 4 HOH A 75 375 36 HOH HOH . G 4 HOH A 76 376 65 HOH HOH . G 4 HOH A 77 377 2 HOH HOH . G 4 HOH A 78 378 145 HOH HOH . G 4 HOH A 79 379 66 HOH HOH . G 4 HOH A 80 380 49 HOH HOH . G 4 HOH A 81 381 143 HOH HOH . G 4 HOH A 82 382 4 HOH HOH . G 4 HOH A 83 383 69 HOH HOH . G 4 HOH A 84 384 26 HOH HOH . H 4 HOH B 1 301 79 HOH HOH . H 4 HOH B 2 302 74 HOH HOH . H 4 HOH B 3 303 75 HOH HOH . H 4 HOH B 4 304 90 HOH HOH . H 4 HOH B 5 305 78 HOH HOH . H 4 HOH B 6 306 130 HOH HOH . H 4 HOH B 7 307 150 HOH HOH . H 4 HOH B 8 308 82 HOH HOH . H 4 HOH B 9 309 85 HOH HOH . H 4 HOH B 10 310 7 HOH HOH . H 4 HOH B 11 311 83 HOH HOH . H 4 HOH B 12 312 86 HOH HOH . H 4 HOH B 13 313 124 HOH HOH . H 4 HOH B 14 314 30 HOH HOH . H 4 HOH B 15 315 147 HOH HOH . H 4 HOH B 16 316 132 HOH HOH . H 4 HOH B 17 317 73 HOH HOH . H 4 HOH B 18 318 133 HOH HOH . H 4 HOH B 19 319 138 HOH HOH . H 4 HOH B 20 320 55 HOH HOH . H 4 HOH B 21 321 137 HOH HOH . H 4 HOH B 22 322 131 HOH HOH . H 4 HOH B 23 323 87 HOH HOH . H 4 HOH B 24 324 125 HOH HOH . H 4 HOH B 25 325 122 HOH HOH . H 4 HOH B 26 326 84 HOH HOH . H 4 HOH B 27 327 41 HOH HOH . H 4 HOH B 28 328 35 HOH HOH . H 4 HOH B 29 329 129 HOH HOH . H 4 HOH B 30 330 37 HOH HOH . H 4 HOH B 31 331 123 HOH HOH . H 4 HOH B 32 332 152 HOH HOH . H 4 HOH B 33 333 34 HOH HOH . H 4 HOH B 34 334 81 HOH HOH . H 4 HOH B 35 335 80 HOH HOH . H 4 HOH B 36 336 135 HOH HOH . H 4 HOH B 37 337 128 HOH HOH . H 4 HOH B 38 338 127 HOH HOH . H 4 HOH B 39 339 153 HOH HOH . H 4 HOH B 40 340 39 HOH HOH . H 4 HOH B 41 341 91 HOH HOH . H 4 HOH B 42 342 126 HOH HOH . H 4 HOH B 43 343 148 HOH HOH . H 4 HOH B 44 344 151 HOH HOH . H 4 HOH B 45 345 136 HOH HOH . H 4 HOH B 46 346 76 HOH HOH . H 4 HOH B 47 347 72 HOH HOH . H 4 HOH B 48 348 104 HOH HOH . H 4 HOH B 49 349 25 HOH HOH . H 4 HOH B 50 350 54 HOH HOH . H 4 HOH B 51 351 88 HOH HOH . H 4 HOH B 52 352 77 HOH HOH . H 4 HOH B 53 353 134 HOH HOH . H 4 HOH B 54 354 149 HOH HOH . H 4 HOH B 55 355 71 HOH HOH . H 4 HOH B 56 356 156 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 . . . D 3 48.912 9.543 5.216 1 14.35 ? P2 THP 202 A 1 HETATM 2 O O4P THP . . . D 3 48.811 8.066 5.369 1 12.97 ? O4P THP 202 A 1 HETATM 3 O O5P THP . . . D 3 47.697 10.286 5.665 1 13.02 ? O5P THP 202 A 1 HETATM 4 O O6P THP . . . D 3 50.215 10.109 5.787 1 15.16 ? O6P THP 202 A 1 HETATM 5 P P1 THP . . . D 3 51.725 13.536 0.418 1 16.62 ? P1 THP 202 A 1 HETATM 6 O O1P THP . . . D 3 50.953 14.027 -0.813 1 24.68 ? O1P THP 202 A 1 HETATM 7 O O2P THP . . . D 3 51.487 14.324 1.61 1 17 ? O2P THP 202 A 1 HETATM 8 O O3P THP . . . D 3 53.139 13.236 -0.016 1 16.12 ? O3P THP 202 A 1 HETATM 9 O O5' THP . . . D 3 48.939 9.712 3.67 1 13.75 ? O5' THP 202 A 1 HETATM 10 C C5' THP . . . D 3 48.793 10.937 2.963 1 16.48 ? C5' THP 202 A 1 HETATM 11 C C4' THP . . . D 3 49.525 10.777 1.644 1 14.51 ? C4' THP 202 A 1 HETATM 12 O O4' THP . . . D 3 48.852 9.808 0.838 1 14.22 ? O4' THP 202 A 1 HETATM 13 C C3' THP . . . D 3 49.609 12.043 0.816 1 15.93 ? C3' THP 202 A 1 HETATM 14 O O3' THP . . . D 3 50.988 12.151 0.412 1 19.1 ? O3' THP 202 A 1 HETATM 15 C C2' THP . . . D 3 48.777 11.746 -0.425 1 15.48 ? C2' THP 202 A 1 HETATM 16 C C1' THP . . . D 3 48.584 10.23 -0.467 1 15.72 ? C1' THP 202 A 1 HETATM 17 N N1 THP . . . D 3 47.216 9.855 -0.847 1 11.84 ? N1 THP 202 A 1 HETATM 18 C C2 THP . . . D 3 46.907 9.821 -2.186 1 14.38 ? C2 THP 202 A 1 HETATM 19 O O2 THP . . . D 3 47.809 10.146 -3.02 1 14.44 ? O2 THP 202 A 1 HETATM 20 N N3 THP . . . D 3 45.648 9.523 -2.591 1 11.77 ? N3 THP 202 A 1 HETATM 21 C C4 THP . . . D 3 44.673 9.169 -1.731 1 12.47 ? C4 THP 202 A 1 HETATM 22 O O4 THP . . . D 3 43.536 8.924 -2.166 1 10.78 ? O4 THP 202 A 1 HETATM 23 C C5 THP . . . D 3 44.978 9.173 -0.307 1 11.18 ? C5 THP 202 A 1 HETATM 24 C C5M THP . . . D 3 43.973 8.761 0.733 1 11.47 ? C5M THP 202 A 1 HETATM 25 C C6 THP . . . D 3 46.286 9.513 0.069 1 12.37 ? C6 THP 202 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #