data_1N5L # _model_server_result.job_id jvETJleoTbnAggTZfV63XA _model_server_result.datetime_utc '2024-10-26 18:27:34' _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 1n5l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":216}' # _entry.id 1N5L # _exptl.entry_id 1N5L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 120 _cell.entry_id 1N5L _cell.length_a 64.454 _cell.length_b 64.454 _cell.length_c 195.899 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1N5L _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 5 _struct_asym.id G _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 B OD1 ASP 9 B ASP 9 1_555 F MG MG . B MG 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc2 F MG MG . B MG 215 1_555 G O2B TYD . B TYD 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc3 F MG MG . B MG 215 1_555 G O2A TYD . B TYD 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc4 F MG MG . B MG 215 1_555 J O HOH . B HOH 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc5 F MG MG . B MG 215 1_555 J O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A TYD doub 385 n n PA O2A TYD sing 386 n n PA O3A TYD sing 387 n n PA O5' TYD sing 388 n n O2A HOA2 TYD sing 389 n n O3A PB TYD sing 390 n n PB O1B TYD doub 391 n n PB O2B TYD sing 392 n n PB O3B TYD sing 393 n n O2B HOB2 TYD sing 394 n n O3B HOB3 TYD sing 395 n n O5' C5' TYD sing 396 n n C5' C4' TYD sing 397 n n C5' "H5'1" TYD sing 398 n n C5' "H5'2" TYD sing 399 n n C4' O4' TYD sing 400 n n C4' C3' TYD sing 401 n n C4' H4' TYD sing 402 n n O4' C1' TYD sing 403 n n C3' O3' TYD sing 404 n n C3' C2' TYD sing 405 n n C3' H3' TYD sing 406 n n O3' HO3' TYD sing 407 n n C2' C1' TYD sing 408 n n C2' "H2'1" TYD sing 409 n n C2' "H2'2" TYD sing 410 n n C1' N1 TYD sing 411 n n C1' H1' TYD sing 412 n n N1 C2 TYD sing 413 n y N1 C6 TYD sing 414 n y C2 O2 TYD doub 415 n n C2 N3 TYD sing 416 n y N3 C4 TYD sing 417 n y N3 HN3 TYD sing 418 n n C4 O4 TYD doub 419 n n C4 C5 TYD sing 420 n y C5 C5M TYD sing 421 n n C5 C6 TYD doub 422 n y C5M H51 TYD sing 423 n n C5M H52 TYD sing 424 n n C5M H53 TYD sing 425 n n C6 H6 TYD sing 426 n n # _atom_sites.entry_id 1N5L _atom_sites.fract_transf_matrix[1][1] 0.015515 _atom_sites.fract_transf_matrix[1][2] 0.008958 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017915 _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] 0.005105 _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 ACT A 1 412 212 ACT ACT . D 2 ACT A 1 413 213 ACT ACT . E 3 TMP A 1 409 209 TMP TMP . F 4 MG B 1 215 210 MG MG . G 5 TYD B 1 216 211 TYD TYD . H 6 DPO B 1 414 214 DPO DPO . I 7 HOH A 1 414 1 HOH TIP . I 7 HOH A 2 415 2 HOH TIP . I 7 HOH A 3 416 3 HOH TIP . I 7 HOH A 4 417 5 HOH TIP . I 7 HOH A 5 418 6 HOH TIP . I 7 HOH A 6 419 12 HOH TIP . I 7 HOH A 7 420 13 HOH TIP . I 7 HOH A 8 421 14 HOH TIP . I 7 HOH A 9 422 15 HOH TIP . I 7 HOH A 10 423 17 HOH TIP . I 7 HOH A 11 424 20 HOH TIP . I 7 HOH A 12 425 22 HOH TIP . I 7 HOH A 13 426 23 HOH TIP . I 7 HOH A 14 427 24 HOH TIP . I 7 HOH A 15 428 25 HOH TIP . I 7 HOH A 16 429 30 HOH TIP . I 7 HOH A 17 430 31 HOH TIP . I 7 HOH A 18 431 32 HOH TIP . I 7 HOH A 19 432 33 HOH TIP . I 7 HOH A 20 433 34 HOH TIP . I 7 HOH A 21 434 35 HOH TIP . I 7 HOH A 22 435 37 HOH TIP . I 7 HOH A 23 436 38 HOH TIP . I 7 HOH A 24 437 39 HOH TIP . I 7 HOH A 25 438 41 HOH TIP . I 7 HOH A 26 439 42 HOH TIP . I 7 HOH A 27 440 43 HOH TIP . I 7 HOH A 28 441 47 HOH TIP . I 7 HOH A 29 442 48 HOH TIP . I 7 HOH A 30 443 50 HOH TIP . I 7 HOH A 31 444 51 HOH TIP . I 7 HOH A 32 445 53 HOH TIP . I 7 HOH A 33 446 55 HOH TIP . I 7 HOH A 34 447 59 HOH TIP . I 7 HOH A 35 448 60 HOH TIP . I 7 HOH A 36 449 61 HOH TIP . I 7 HOH A 37 450 64 HOH TIP . I 7 HOH A 38 451 65 HOH TIP . I 7 HOH A 39 452 66 HOH TIP . I 7 HOH A 40 453 67 HOH TIP . I 7 HOH A 41 454 69 HOH TIP . I 7 HOH A 42 455 71 HOH TIP . I 7 HOH A 43 456 72 HOH TIP . I 7 HOH A 44 457 77 HOH TIP . I 7 HOH A 45 458 79 HOH TIP . I 7 HOH A 46 459 80 HOH TIP . I 7 HOH A 47 460 82 HOH TIP . I 7 HOH A 48 461 83 HOH TIP . I 7 HOH A 49 462 85 HOH TIP . I 7 HOH A 50 463 89 HOH TIP . I 7 HOH A 51 464 94 HOH TIP . I 7 HOH A 52 465 96 HOH TIP . I 7 HOH A 53 466 97 HOH TIP . I 7 HOH A 54 467 98 HOH TIP . I 7 HOH A 55 468 99 HOH TIP . I 7 HOH A 56 469 103 HOH TIP . I 7 HOH A 57 470 104 HOH TIP . I 7 HOH A 58 471 105 HOH TIP . I 7 HOH A 59 472 106 HOH TIP . I 7 HOH A 60 473 107 HOH TIP . I 7 HOH A 61 474 109 HOH TIP . I 7 HOH A 62 475 110 HOH TIP . I 7 HOH A 63 476 111 HOH TIP . I 7 HOH A 64 477 114 HOH TIP . I 7 HOH A 65 478 116 HOH TIP . I 7 HOH A 66 479 117 HOH TIP . I 7 HOH A 67 480 118 HOH TIP . I 7 HOH A 68 481 119 HOH TIP . I 7 HOH A 69 482 121 HOH TIP . I 7 HOH A 70 483 122 HOH TIP . I 7 HOH A 71 484 125 HOH TIP . I 7 HOH A 72 485 128 HOH TIP . I 7 HOH A 73 486 131 HOH TIP . I 7 HOH A 74 487 132 HOH TIP . I 7 HOH A 75 488 133 HOH TIP . I 7 HOH A 76 489 134 HOH TIP . I 7 HOH A 77 490 136 HOH TIP . I 7 HOH A 78 491 137 HOH TIP . I 7 HOH A 79 492 140 HOH TIP . I 7 HOH A 80 493 142 HOH TIP . I 7 HOH A 81 494 144 HOH TIP . I 7 HOH A 82 495 145 HOH TIP . I 7 HOH A 83 496 147 HOH TIP . I 7 HOH A 84 497 149 HOH TIP . I 7 HOH A 85 498 150 HOH TIP . I 7 HOH A 86 499 151 HOH TIP . I 7 HOH A 87 500 156 HOH TIP . I 7 HOH A 88 501 158 HOH TIP . I 7 HOH A 89 502 159 HOH TIP . I 7 HOH A 90 503 161 HOH TIP . I 7 HOH A 91 504 163 HOH TIP . I 7 HOH A 92 505 166 HOH TIP . I 7 HOH A 93 506 174 HOH TIP . I 7 HOH A 94 507 178 HOH TIP . I 7 HOH A 95 508 179 HOH TIP . I 7 HOH A 96 509 181 HOH TIP . I 7 HOH A 97 510 189 HOH TIP . I 7 HOH A 98 511 195 HOH TIP . I 7 HOH A 99 512 196 HOH TIP . I 7 HOH A 100 513 198 HOH TIP . I 7 HOH A 101 514 299 HOH TIP . I 7 HOH A 102 515 200 HOH TIP . I 7 HOH A 103 516 201 HOH TIP . I 7 HOH A 104 517 205 HOH TIP . I 7 HOH A 105 518 209 HOH TIP . I 7 HOH A 106 519 210 HOH TIP . I 7 HOH A 107 520 213 HOH TIP . I 7 HOH A 108 521 215 HOH TIP . I 7 HOH A 109 522 216 HOH TIP . I 7 HOH A 110 523 222 HOH TIP . I 7 HOH A 111 524 225 HOH TIP . I 7 HOH A 112 525 226 HOH TIP . I 7 HOH A 113 526 230 HOH TIP . I 7 HOH A 114 527 231 HOH TIP . I 7 HOH A 115 528 232 HOH TIP . I 7 HOH A 116 529 235 HOH TIP . I 7 HOH A 117 530 236 HOH TIP . J 7 HOH B 1 415 4 HOH TIP . J 7 HOH B 2 416 7 HOH TIP . J 7 HOH B 3 417 8 HOH TIP . J 7 HOH B 4 418 9 HOH TIP . J 7 HOH B 5 419 10 HOH TIP . J 7 HOH B 6 420 11 HOH TIP . J 7 HOH B 7 421 16 HOH TIP . J 7 HOH B 8 422 18 HOH TIP . J 7 HOH B 9 423 19 HOH TIP . J 7 HOH B 10 424 21 HOH TIP . J 7 HOH B 11 425 26 HOH TIP . J 7 HOH B 12 426 27 HOH TIP . J 7 HOH B 13 427 28 HOH TIP . J 7 HOH B 14 428 29 HOH TIP . J 7 HOH B 15 429 36 HOH TIP . J 7 HOH B 16 430 40 HOH TIP . J 7 HOH B 17 431 44 HOH TIP . J 7 HOH B 18 432 45 HOH TIP . J 7 HOH B 19 433 46 HOH TIP . J 7 HOH B 20 434 49 HOH TIP . J 7 HOH B 21 435 54 HOH TIP . J 7 HOH B 22 436 56 HOH TIP . J 7 HOH B 23 437 57 HOH TIP . J 7 HOH B 24 438 58 HOH TIP . J 7 HOH B 25 439 62 HOH TIP . J 7 HOH B 26 440 63 HOH TIP . J 7 HOH B 27 441 68 HOH TIP . J 7 HOH B 28 442 70 HOH TIP . J 7 HOH B 29 443 74 HOH TIP . J 7 HOH B 30 444 75 HOH TIP . J 7 HOH B 31 445 76 HOH TIP . J 7 HOH B 32 446 78 HOH TIP . J 7 HOH B 33 447 81 HOH TIP . J 7 HOH B 34 448 84 HOH TIP . J 7 HOH B 35 449 86 HOH TIP . J 7 HOH B 36 450 87 HOH TIP . J 7 HOH B 37 451 88 HOH TIP . J 7 HOH B 38 452 92 HOH TIP . J 7 HOH B 39 453 93 HOH TIP . J 7 HOH B 40 454 100 HOH TIP . J 7 HOH B 41 455 101 HOH TIP . J 7 HOH B 42 456 102 HOH TIP . J 7 HOH B 43 457 108 HOH TIP . J 7 HOH B 44 458 112 HOH TIP . J 7 HOH B 45 459 113 HOH TIP . J 7 HOH B 46 460 115 HOH TIP . J 7 HOH B 47 461 120 HOH TIP . J 7 HOH B 48 462 123 HOH TIP . J 7 HOH B 49 463 126 HOH TIP . J 7 HOH B 50 464 127 HOH TIP . J 7 HOH B 51 465 129 HOH TIP . J 7 HOH B 52 466 135 HOH TIP . J 7 HOH B 53 467 138 HOH TIP . J 7 HOH B 54 468 139 HOH TIP . J 7 HOH B 55 469 140 HOH TIP . J 7 HOH B 56 470 148 HOH TIP . J 7 HOH B 57 471 152 HOH TIP . J 7 HOH B 58 472 154 HOH TIP . J 7 HOH B 59 473 155 HOH TIP . J 7 HOH B 60 474 157 HOH TIP . J 7 HOH B 61 475 164 HOH TIP . J 7 HOH B 62 476 167 HOH TIP . J 7 HOH B 63 477 168 HOH TIP . J 7 HOH B 64 478 171 HOH TIP . J 7 HOH B 65 479 172 HOH TIP . J 7 HOH B 66 480 175 HOH TIP . J 7 HOH B 67 481 177 HOH TIP . J 7 HOH B 68 482 180 HOH TIP . J 7 HOH B 69 483 182 HOH TIP . J 7 HOH B 70 484 187 HOH TIP . J 7 HOH B 71 485 188 HOH TIP . J 7 HOH B 72 486 190 HOH TIP . J 7 HOH B 73 487 191 HOH TIP . J 7 HOH B 74 488 192 HOH TIP . J 7 HOH B 75 489 193 HOH TIP . J 7 HOH B 76 490 194 HOH TIP . J 7 HOH B 77 491 197 HOH TIP . J 7 HOH B 78 492 203 HOH TIP . J 7 HOH B 79 493 204 HOH TIP . J 7 HOH B 80 494 207 HOH TIP . J 7 HOH B 81 495 208 HOH TIP . J 7 HOH B 82 496 214 HOH TIP . J 7 HOH B 83 497 217 HOH TIP . J 7 HOH B 84 498 218 HOH TIP . J 7 HOH B 85 499 223 HOH TIP . J 7 HOH B 86 500 228 HOH TIP . J 7 HOH B 87 501 233 HOH TIP . J 7 HOH B 88 502 237 HOH TIP . # 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 PA TYD . . . G 5 38.191 31.66 57.068 1 38.91 ? PA TYD 216 B 1 HETATM 2 O O1A TYD . . . G 5 38.729 33.076 57.109 1 40.34 ? O1A TYD 216 B 1 HETATM 3 O O2A TYD . . . G 5 37.422 31.217 55.92 1 36.97 ? O2A TYD 216 B 1 HETATM 4 O O3A TYD . . . G 5 39.411 30.63 57.244 1 43.23 ? O3A TYD 216 B 1 HETATM 5 P PB TYD . . . G 5 40.222 29.621 56.262 1 50.07 ? PB TYD 216 B 1 HETATM 6 O O1B TYD . . . G 5 41.454 30.37 55.967 1 50.46 ? O1B TYD 216 B 1 HETATM 7 O O2B TYD . . . G 5 39.39 29.421 55.015 1 50.65 ? O2B TYD 216 B 1 HETATM 8 O O3B TYD . . . G 5 40.403 28.43 57.086 1 49.29 ? O3B TYD 216 B 1 HETATM 9 O O5' TYD . . . G 5 37.294 31.434 58.39 1 37.27 ? O5' TYD 216 B 1 HETATM 10 C C5' TYD . . . G 5 36.924 30.098 58.784 1 32.35 ? C5' TYD 216 B 1 HETATM 11 C C4' TYD . . . G 5 35.44 29.828 58.642 1 33.44 ? C4' TYD 216 B 1 HETATM 12 O O4' TYD . . . G 5 34.736 30.269 59.789 1 32.93 ? O4' TYD 216 B 1 HETATM 13 C C3' TYD . . . G 5 34.707 30.463 57.439 1 32.49 ? C3' TYD 216 B 1 HETATM 14 O O3' TYD . . . G 5 33.876 29.391 57.007 1 32.9 ? O3' TYD 216 B 1 HETATM 15 C C2' TYD . . . G 5 33.971 31.654 57.994 1 31.27 ? C2' TYD 216 B 1 HETATM 16 C C1' TYD . . . G 5 33.796 31.324 59.492 1 30 ? C1' TYD 216 B 1 HETATM 17 N N1 TYD . . . G 5 33.986 32.504 60.407 1 30.07 ? N1 TYD 216 B 1 HETATM 18 C C2 TYD . . . G 5 32.937 32.822 61.302 1 28.78 ? C2 TYD 216 B 1 HETATM 19 O O2 TYD . . . G 5 31.895 32.163 61.352 1 27.37 ? O2 TYD 216 B 1 HETATM 20 N N3 TYD . . . G 5 33.138 33.941 62.144 1 27.35 ? N3 TYD 216 B 1 HETATM 21 C C4 TYD . . . G 5 34.288 34.744 62.158 1 26.93 ? C4 TYD 216 B 1 HETATM 22 O O4 TYD . . . G 5 34.341 35.689 62.935 1 28.31 ? O4 TYD 216 B 1 HETATM 23 C C5 TYD . . . G 5 35.332 34.351 61.208 1 26.75 ? C5 TYD 216 B 1 HETATM 24 C C5M TYD . . . G 5 36.639 35.133 61.118 1 25.45 ? C5M TYD 216 B 1 HETATM 25 C C6 TYD . . . G 5 35.162 33.28 60.387 1 27.94 ? C6 TYD 216 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #