data_3RCB # _model_server_result.job_id 22KLRO-gIo6oTvGdGpA9Dw _model_server_result.datetime_utc '2024-11-26 00:22:54' _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 3rcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":337}' # _entry.id 3RCB # _exptl.entry_id 3RCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 478.284 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine" _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 3RCB _cell.length_a 72.371 _cell.length_b 103.497 _cell.length_c 145.154 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 G 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 O ARG 341 A ARG 323 1_555 D NA NA . A NA 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc2 A O THR 342 A THR 324 1_555 D NA NA . A NA 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc3 A O ALA 344 A ALA 326 1_555 D NA NA . A NA 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc4 A OD2 ASP 346 A ASP 328 1_555 D NA NA . A NA 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc5 D NA NA . A NA 335 1_555 H O HOH . A HOH 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? # _chem_comp.formula 'C16 H20 N2 O11 P2' _chem_comp.formula_weight 478.284 _chem_comp.id TLO _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'thymidine diphosphate phenol' # 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 C1' N1 TLO sing 390 n n N1 C6 TLO sing 391 n n N1 C2 TLO sing 392 n n O2 C2 TLO doub 393 n n C2 N3 TLO sing 394 n n N3 C4 TLO sing 395 n n N3 HN3 TLO sing 396 n n C5 C4 TLO sing 397 n n C4 O4 TLO doub 398 n n C6 C5 TLO doub 399 n n C5 C5M TLO sing 400 n n C6 H6 TLO sing 401 n n O3A PA TLO sing 402 n n O2A PA TLO doub 403 n n PA O5' TLO sing 404 n n PA O1A TLO sing 405 n n O3B PB TLO sing 406 n n O2B PB TLO doub 407 n n PB O1B TLO sing 408 n n PB O3A TLO sing 409 n n CD2 CG TLO doub 410 n y CG O3B TLO sing 411 n n CG CD1 TLO sing 412 n y CE2 CZ TLO doub 413 n y CZ CE1 TLO sing 414 n y CZ HZ TLO sing 415 n n C2' C1' TLO sing 416 n n C1' O4' TLO sing 417 n n C1' H1' TLO sing 418 n n O1A HO1A TLO sing 419 n n O1B HO1B TLO sing 420 n n C3' C2' TLO sing 421 n n C2' H2' TLO sing 422 n n C2' "H2'A" TLO sing 423 n n O3' C3' TLO sing 424 n n C3' C4' TLO sing 425 n n C3' H3' TLO sing 426 n n O3' HO3' TLO sing 427 n n C5' C4' TLO sing 428 n n C4' O4' TLO sing 429 n n C4' H4' TLO sing 430 n n O5' C5' TLO sing 431 n n C5' H5' TLO sing 432 n n C5' "H5'A" TLO sing 433 n n C5M H5M TLO sing 434 n n C5M H5MA TLO sing 435 n n C5M H5MB TLO sing 436 n n CE1 CD1 TLO doub 437 n y CD1 HD1 TLO sing 438 n n CE2 CD2 TLO sing 439 n y CD2 HD2 TLO sing 440 n n CE1 HE1 TLO sing 441 n n CE2 HE2 TLO sing 442 n n # _atom_sites.entry_id 3RCB _atom_sites.fract_transf_matrix[1][1] 0.013818 _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] 0.009662 _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] 0.006889 _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 NAP A 1 333 1 NAP NAP . C 3 CL A 1 334 1 CL CL . D 4 NA A 1 335 1 NA NA . E 5 PO4 A 1 336 1 PO4 PO4 . F 6 TLO A 1 337 301 TLO TLO . G 6 TLO A 1 338 301 TLO TLO . H 7 HOH A 1 339 1 HOH HOH . H 7 HOH A 2 340 2 HOH HOH . H 7 HOH A 3 341 3 HOH HOH . H 7 HOH A 4 342 5 HOH HOH . H 7 HOH A 5 343 6 HOH HOH . H 7 HOH A 6 344 7 HOH HOH . H 7 HOH A 7 345 8 HOH HOH . H 7 HOH A 8 346 9 HOH HOH . H 7 HOH A 9 347 10 HOH HOH . H 7 HOH A 10 348 11 HOH HOH . H 7 HOH A 11 349 12 HOH HOH . H 7 HOH A 12 350 13 HOH HOH . H 7 HOH A 13 351 14 HOH HOH . H 7 HOH A 14 352 15 HOH HOH . H 7 HOH A 15 353 17 HOH HOH . H 7 HOH A 16 354 18 HOH HOH . H 7 HOH A 17 355 19 HOH HOH . H 7 HOH A 18 356 20 HOH HOH . H 7 HOH A 19 357 21 HOH HOH . H 7 HOH A 20 358 22 HOH HOH . H 7 HOH A 21 359 25 HOH HOH . H 7 HOH A 22 360 27 HOH HOH . H 7 HOH A 23 361 29 HOH HOH . H 7 HOH A 24 362 30 HOH HOH . H 7 HOH A 25 363 31 HOH HOH . H 7 HOH A 26 364 32 HOH HOH . H 7 HOH A 27 365 33 HOH HOH . H 7 HOH A 28 366 34 HOH HOH . H 7 HOH A 29 367 35 HOH HOH . H 7 HOH A 30 368 36 HOH HOH . H 7 HOH A 31 369 37 HOH HOH . H 7 HOH A 32 370 38 HOH HOH . H 7 HOH A 33 371 40 HOH HOH . H 7 HOH A 34 372 41 HOH HOH . H 7 HOH A 35 373 42 HOH HOH . H 7 HOH A 36 374 43 HOH HOH . H 7 HOH A 37 375 44 HOH HOH . H 7 HOH A 38 376 45 HOH HOH . H 7 HOH A 39 377 46 HOH HOH . H 7 HOH A 40 378 47 HOH HOH . H 7 HOH A 41 379 48 HOH HOH . H 7 HOH A 42 380 50 HOH HOH . H 7 HOH A 43 381 51 HOH HOH . H 7 HOH A 44 382 52 HOH HOH . H 7 HOH A 45 383 54 HOH HOH . H 7 HOH A 46 384 57 HOH HOH . H 7 HOH A 47 385 59 HOH HOH . H 7 HOH A 48 386 60 HOH HOH . H 7 HOH A 49 387 61 HOH HOH . H 7 HOH A 50 388 63 HOH HOH . H 7 HOH A 51 389 64 HOH HOH . H 7 HOH A 52 390 65 HOH HOH . H 7 HOH A 53 391 67 HOH HOH . H 7 HOH A 54 392 68 HOH HOH . H 7 HOH A 55 393 69 HOH HOH . H 7 HOH A 56 394 70 HOH HOH . H 7 HOH A 57 395 71 HOH HOH . H 7 HOH A 58 396 74 HOH HOH . H 7 HOH A 59 397 76 HOH HOH . H 7 HOH A 60 398 77 HOH HOH . H 7 HOH A 61 399 78 HOH HOH . H 7 HOH A 62 400 79 HOH HOH . H 7 HOH A 63 401 80 HOH HOH . H 7 HOH A 64 402 81 HOH HOH . H 7 HOH A 65 403 82 HOH HOH . H 7 HOH A 66 404 83 HOH HOH . H 7 HOH A 67 405 84 HOH HOH . H 7 HOH A 68 406 86 HOH HOH . H 7 HOH A 69 407 87 HOH HOH . H 7 HOH A 70 408 89 HOH HOH . H 7 HOH A 71 409 90 HOH HOH . H 7 HOH A 72 410 91 HOH HOH . H 7 HOH A 73 411 93 HOH HOH . H 7 HOH A 74 412 94 HOH HOH . H 7 HOH A 75 413 97 HOH HOH . H 7 HOH A 76 414 98 HOH HOH . H 7 HOH A 77 415 100 HOH HOH . H 7 HOH A 78 416 102 HOH HOH . H 7 HOH A 79 417 103 HOH HOH . H 7 HOH A 80 418 104 HOH HOH . H 7 HOH A 81 419 105 HOH HOH . H 7 HOH A 82 420 107 HOH HOH . H 7 HOH A 83 421 110 HOH HOH . H 7 HOH A 84 422 114 HOH HOH . H 7 HOH A 85 423 115 HOH HOH . H 7 HOH A 86 424 116 HOH HOH . H 7 HOH A 87 425 117 HOH HOH . H 7 HOH A 88 426 118 HOH HOH . H 7 HOH A 89 427 119 HOH HOH . H 7 HOH A 90 428 120 HOH HOH . H 7 HOH A 91 429 122 HOH HOH . H 7 HOH A 92 430 123 HOH HOH . H 7 HOH A 93 431 125 HOH HOH . H 7 HOH A 94 432 127 HOH HOH . H 7 HOH A 95 433 129 HOH HOH . H 7 HOH A 96 434 130 HOH HOH . H 7 HOH A 97 435 132 HOH HOH . H 7 HOH A 98 436 134 HOH HOH . H 7 HOH A 99 437 135 HOH HOH . H 7 HOH A 100 438 136 HOH HOH . H 7 HOH A 101 439 137 HOH HOH . H 7 HOH A 102 440 138 HOH HOH . H 7 HOH A 103 441 139 HOH HOH . H 7 HOH A 104 442 144 HOH HOH . H 7 HOH A 105 443 152 HOH HOH . H 7 HOH A 106 444 156 HOH HOH . H 7 HOH A 107 445 162 HOH HOH . H 7 HOH A 108 446 165 HOH HOH . H 7 HOH A 109 447 169 HOH HOH . H 7 HOH A 110 448 171 HOH HOH . H 7 HOH A 111 449 172 HOH HOH . H 7 HOH A 112 450 173 HOH HOH . H 7 HOH A 113 451 174 HOH HOH . H 7 HOH A 114 452 175 HOH HOH . H 7 HOH A 115 453 177 HOH HOH . H 7 HOH A 116 454 179 HOH HOH . H 7 HOH A 117 455 180 HOH HOH . H 7 HOH A 118 456 181 HOH HOH . H 7 HOH A 119 457 182 HOH HOH . H 7 HOH A 120 458 184 HOH HOH . H 7 HOH A 121 459 185 HOH HOH . H 7 HOH A 122 460 186 HOH HOH . H 7 HOH A 123 461 189 HOH HOH . H 7 HOH A 124 462 190 HOH HOH . H 7 HOH A 125 463 191 HOH HOH . H 7 HOH A 126 464 192 HOH HOH . H 7 HOH A 127 465 193 HOH HOH . H 7 HOH A 128 466 194 HOH HOH . H 7 HOH A 129 467 195 HOH HOH . H 7 HOH A 130 468 196 HOH HOH . H 7 HOH A 131 469 198 HOH HOH . H 7 HOH A 132 470 199 HOH HOH . H 7 HOH A 133 471 200 HOH HOH . H 7 HOH A 134 472 201 HOH HOH . H 7 HOH A 135 473 202 HOH HOH . H 7 HOH A 136 474 203 HOH HOH . H 7 HOH A 137 475 204 HOH HOH . H 7 HOH A 138 476 205 HOH HOH . H 7 HOH A 139 477 206 HOH HOH . H 7 HOH A 140 478 207 HOH HOH . H 7 HOH A 141 479 208 HOH HOH . H 7 HOH A 142 480 209 HOH HOH . H 7 HOH A 143 481 210 HOH HOH . H 7 HOH A 144 482 211 HOH HOH . H 7 HOH A 145 483 212 HOH HOH . H 7 HOH A 146 484 213 HOH HOH . H 7 HOH A 147 485 214 HOH HOH . H 7 HOH A 148 486 215 HOH HOH . H 7 HOH A 149 487 216 HOH HOH . H 7 HOH A 150 488 217 HOH HOH . H 7 HOH A 151 489 218 HOH HOH . H 7 HOH A 152 490 219 HOH HOH . H 7 HOH A 153 491 220 HOH HOH . H 7 HOH A 154 492 221 HOH HOH . H 7 HOH A 155 493 222 HOH HOH . H 7 HOH A 156 494 223 HOH HOH . H 7 HOH A 157 495 224 HOH HOH . H 7 HOH A 158 496 225 HOH HOH . H 7 HOH A 159 497 226 HOH HOH . H 7 HOH A 160 498 227 HOH HOH . H 7 HOH A 161 499 228 HOH HOH . H 7 HOH A 162 500 229 HOH HOH . H 7 HOH A 163 501 230 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 N N1 TLO . . . F 6 -45.545 -11.142 -15.912 1 17.79 ? N1 TLO 337 A 1 HETATM 2 C C2 TLO . . . F 6 -46.179 -10.77 -14.795 1 17.88 ? C2 TLO 337 A 1 HETATM 3 O O2 TLO . . . F 6 -47.173 -11.438 -14.457 1 17.46 ? O2 TLO 337 A 1 HETATM 4 N N3 TLO . . . F 6 -45.774 -9.712 -14.058 1 19.4 ? N3 TLO 337 A 1 HETATM 5 C C4 TLO . . . F 6 -44.665 -9.048 -14.475 1 21.52 ? C4 TLO 337 A 1 HETATM 6 O O4 TLO . . . F 6 -44.223 -8.067 -13.84 1 18.63 ? O4 TLO 337 A 1 HETATM 7 C C5 TLO . . . F 6 -43.982 -9.418 -15.632 1 18.9 ? C5 TLO 337 A 1 HETATM 8 C C6 TLO . . . F 6 -44.455 -10.504 -16.349 1 13.34 ? C6 TLO 337 A 1 HETATM 9 P PA TLO . . . F 6 -41.458 -12.561 -18.4 1 16.19 ? PA TLO 337 A 1 HETATM 10 P PB TLO . . . F 6 -41.101 -13.89 -20.959 1 24.86 ? PB TLO 337 A 1 HETATM 11 C CG TLO . . . F 6 -41.517 -16.388 -20.305 1 22.85 ? CG TLO 337 A 1 HETATM 12 C CZ TLO . . . F 6 -42.254 -18.302 -18.498 1 24.25 ? CZ TLO 337 A 1 HETATM 13 C C1' TLO . . . F 6 -46.055 -12.305 -16.655 1 15.64 ? C1' TLO 337 A 1 HETATM 14 O O1A TLO . . . F 6 -41.538 -11.188 -18.972 1 16.83 ? O1A TLO 337 A 1 HETATM 15 O O1B TLO . . . F 6 -39.845 -13.315 -21.571 1 26.6 ? O1B TLO 337 A 1 HETATM 16 C C2' TLO . . . F 6 -46.152 -12.105 -18.165 1 11.13 ? C2' TLO 337 A 1 HETATM 17 O O2A TLO . . . F 6 -40.716 -12.778 -17.112 1 22.23 ? O2A TLO 337 A 1 HETATM 18 O O2B TLO . . . F 6 -42.445 -13.456 -21.482 1 26.97 ? O2B TLO 337 A 1 HETATM 19 C C3' TLO . . . F 6 -45.779 -13.489 -18.667 1 16.04 ? C3' TLO 337 A 1 HETATM 20 O O3' TLO . . . F 6 -46.889 -14.4 -18.673 1 14.52 ? O3' TLO 337 A 1 HETATM 21 O O3A TLO . . . F 6 -41.025 -13.789 -19.348 1 25.24 ? O3A TLO 337 A 1 HETATM 22 O O3B TLO . . . F 6 -41.099 -15.465 -21.2 1 23.3 ? O3B TLO 337 A 1 HETATM 23 C C4' TLO . . . F 6 -44.899 -14.146 -17.61 1 16.83 ? C4' TLO 337 A 1 HETATM 24 O O4' TLO . . . F 6 -45.147 -13.391 -16.432 1 16.59 ? O4' TLO 337 A 1 HETATM 25 C C5' TLO . . . F 6 -43.432 -14.22 -18.009 1 17.52 ? C5' TLO 337 A 1 HETATM 26 O O5' TLO . . . F 6 -43.031 -12.872 -18.246 1 21.38 ? O5' TLO 337 A 1 HETATM 27 C C5M TLO . . . F 6 -42.753 -8.662 -16.087 1 11 ? C5M TLO 337 A 1 HETATM 28 C CD1 TLO . . . F 6 -42.831 -16.853 -20.302 1 25.22 ? CD1 TLO 337 A 1 HETATM 29 C CD2 TLO . . . F 6 -40.529 -16.85 -19.453 1 20.72 ? CD2 TLO 337 A 1 HETATM 30 C CE1 TLO . . . F 6 -43.216 -17.836 -19.389 1 24.07 ? CE1 TLO 337 A 1 HETATM 31 C CE2 TLO . . . F 6 -40.95 -17.812 -18.54 1 24.8 ? CE2 TLO 337 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #