data_2GDE # _model_server_result.job_id khh6akdgBxRflO7VNEcZ1Q _model_server_result.datetime_utc '2025-07-03 19:48:43' _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 2gde # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 2GDE # _exptl.entry_id 2GDE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 667.172 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(R)-3-((2S,3R)-1-((2S,3AR,5S,6S,7AS)-2-(2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYLCARBAMOYL)-5,6-DIHYDROXYOCTA HYDRO-1H-INDOL-1-YL)-3-CHLORO-4-METHYL-1-OXOPENTAN-2-YLAMINO)-2-METHOXY-3-OXOPROPYL HYDROGEN SULFATE' _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 99.06 _cell.angle_gamma 90 _cell.entry_id 2GDE _cell.length_a 70.084 _cell.length_b 72.169 _cell.length_c 70.357 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GDE _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 E _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 disulf ? disulf1 A SG CYS 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 C C GLU 8 D GLU 362 1_555 C N TYS 9 D TYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 C C TYS 9 D TYS 363 1_555 C N LEU 10 D LEU 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? metalc ? metalc1 D NA NA . H NA 402 1_555 G O HOH . H HOH 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? # _chem_comp.formula 'C26 H43 Cl N6 O10 S' _chem_comp.formula_weight 667.172 _chem_comp.id SN3 _chem_comp.mon_nstd_flag . _chem_comp.name '(R)-3-((2S,3R)-1-((2S,3AR,5S,6S,7AS)-2-(2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYLCARBAMOYL)-5,6-DIHYDROXYOCTA HYDRO-1H-INDOL-1-YL)-3-CHLORO-4-METHYL-1-OXOPENTAN-2-YLAMINO)-2-METHOXY-3-OXOPROPYL HYDROGEN SULFATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CHLORODYSINOSIN # 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 C2 SN3 sing 290 n n C1 C6 SN3 sing 291 n n C1 O46 SN3 sing 292 n n C1 H1 SN3 sing 293 n n C2 C3 SN3 sing 294 n n C2 H21 SN3 sing 295 n n C2 H22 SN3 sing 296 n n C3 C4 SN3 sing 297 n n C3 C10 SN3 sing 298 n n C3 H3 SN3 sing 299 n n C4 C5 SN3 sing 300 n n C4 N8 SN3 sing 301 n n C4 H4 SN3 sing 302 n n C5 C6 SN3 sing 303 n n C5 H51 SN3 sing 304 n n C5 H52 SN3 sing 305 n n C6 O7 SN3 sing 306 n n C6 H6 SN3 sing 307 n n O7 HO7 SN3 sing 308 n n N8 C9 SN3 sing 309 n n N8 C24 SN3 sing 310 n n C9 C10 SN3 sing 311 n n C9 C11 SN3 sing 312 n n C9 H9 SN3 sing 313 n n C10 H101 SN3 sing 314 n n C10 H102 SN3 sing 315 n n C11 N12 SN3 sing 316 n n C11 O23 SN3 doub 317 n n N12 C13 SN3 sing 318 n n N12 HN12 SN3 sing 319 n n C13 C14 SN3 sing 320 n n C13 H131 SN3 sing 321 n n C13 H132 SN3 sing 322 n n C14 C15 SN3 sing 323 n n C14 H141 SN3 sing 324 n n C14 H142 SN3 sing 325 n n C15 C16 SN3 sing 326 n n C15 C19 SN3 doub 327 n n C16 N17 SN3 sing 328 n n C16 H161 SN3 sing 329 n n C16 H162 SN3 sing 330 n n N17 C18 SN3 sing 331 n n N17 C20 SN3 sing 332 n n C18 C19 SN3 sing 333 n n C18 H181 SN3 sing 334 n n C18 H182 SN3 sing 335 n n C19 H192 SN3 sing 336 n n C20 N21 SN3 doub 337 n n C20 N22 SN3 sing 338 n n N21 HN21 SN3 sing 339 n n N22 H221 SN3 sing 340 n n N22 H222 SN3 sing 341 n n C24 O25 SN3 doub 342 n n C24 C26 SN3 sing 343 n n C26 C27 SN3 sing 344 n n C26 N32 SN3 sing 345 n n C26 H26 SN3 sing 346 n n C27 C28 SN3 sing 347 n n C27 CL31 SN3 sing 348 n n C27 H27 SN3 sing 349 n n C28 C29 SN3 sing 350 n n C28 C30 SN3 sing 351 n n C28 H28 SN3 sing 352 n n C29 H291 SN3 sing 353 n n C29 H292 SN3 sing 354 n n C29 H293 SN3 sing 355 n n C30 H301 SN3 sing 356 n n C30 H302 SN3 sing 357 n n C30 H303 SN3 sing 358 n n N32 C33 SN3 sing 359 n n N32 HN32 SN3 sing 360 n n C33 C34 SN3 sing 361 n n C33 O43 SN3 doub 362 n n C34 O35 SN3 sing 363 n n C34 C37 SN3 sing 364 n n C34 H34 SN3 sing 365 n n O35 C36 SN3 sing 366 n n C36 H361 SN3 sing 367 n n C36 H362 SN3 sing 368 n n C36 H363 SN3 sing 369 n n C37 O38 SN3 sing 370 n n C37 H371 SN3 sing 371 n n C37 H372 SN3 sing 372 n n O38 S39 SN3 sing 373 n n S39 O40 SN3 sing 374 n n S39 O41 SN3 doub 375 n n S39 O42 SN3 doub 376 n n O40 HO40 SN3 sing 377 n n O46 HO46 SN3 sing 378 n n # _atom_sites.entry_id 2GDE _atom_sites.fract_transf_matrix[1][1] 0.01427 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00228 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01386 _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] 0.01439 _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 D 4 NA H 1 402 402 NA NA . E 5 SN3 H 1 401 401 SN3 SN3 . F 6 HOH L 1 18 12 HOH HOH . F 6 HOH L 2 19 35 HOH HOH . F 6 HOH L 3 20 51 HOH HOH . F 6 HOH L 4 21 64 HOH HOH . F 6 HOH L 5 22 78 HOH HOH . F 6 HOH L 6 23 79 HOH HOH . G 6 HOH H 1 403 1 HOH HOH . G 6 HOH H 2 404 2 HOH HOH . G 6 HOH H 3 405 3 HOH HOH . G 6 HOH H 4 406 4 HOH HOH . G 6 HOH H 5 407 5 HOH HOH . G 6 HOH H 6 408 6 HOH HOH . G 6 HOH H 7 409 7 HOH HOH . G 6 HOH H 8 410 8 HOH HOH . G 6 HOH H 9 411 9 HOH HOH . G 6 HOH H 10 412 10 HOH HOH . G 6 HOH H 11 413 11 HOH HOH . G 6 HOH H 12 414 13 HOH HOH . G 6 HOH H 13 415 14 HOH HOH . G 6 HOH H 14 416 15 HOH HOH . G 6 HOH H 15 417 16 HOH HOH . G 6 HOH H 16 418 17 HOH HOH . G 6 HOH H 17 419 18 HOH HOH . G 6 HOH H 18 420 19 HOH HOH . G 6 HOH H 19 421 20 HOH HOH . G 6 HOH H 20 422 21 HOH HOH . G 6 HOH H 21 423 22 HOH HOH . G 6 HOH H 22 424 23 HOH HOH . G 6 HOH H 23 425 24 HOH HOH . G 6 HOH H 24 426 25 HOH HOH . G 6 HOH H 25 427 26 HOH HOH . G 6 HOH H 26 428 27 HOH HOH . G 6 HOH H 27 429 28 HOH HOH . G 6 HOH H 28 430 29 HOH HOH . G 6 HOH H 29 431 30 HOH HOH . G 6 HOH H 30 432 31 HOH HOH . G 6 HOH H 31 433 32 HOH HOH . G 6 HOH H 32 434 33 HOH HOH . G 6 HOH H 33 435 34 HOH HOH . G 6 HOH H 34 436 36 HOH HOH . G 6 HOH H 35 437 37 HOH HOH . G 6 HOH H 36 438 38 HOH HOH . G 6 HOH H 37 439 39 HOH HOH . G 6 HOH H 38 440 40 HOH HOH . G 6 HOH H 39 441 41 HOH HOH . G 6 HOH H 40 442 42 HOH HOH . G 6 HOH H 41 443 43 HOH HOH . G 6 HOH H 42 444 44 HOH HOH . G 6 HOH H 43 445 45 HOH HOH . G 6 HOH H 44 446 46 HOH HOH . G 6 HOH H 45 447 47 HOH HOH . G 6 HOH H 46 448 48 HOH HOH . G 6 HOH H 47 449 49 HOH HOH . G 6 HOH H 48 450 50 HOH HOH . G 6 HOH H 49 451 52 HOH HOH . G 6 HOH H 50 452 53 HOH HOH . G 6 HOH H 51 453 54 HOH HOH . G 6 HOH H 52 454 55 HOH HOH . G 6 HOH H 53 455 56 HOH HOH . G 6 HOH H 54 456 57 HOH HOH . G 6 HOH H 55 457 58 HOH HOH . G 6 HOH H 56 458 59 HOH HOH . G 6 HOH H 57 459 60 HOH HOH . G 6 HOH H 58 460 61 HOH HOH . G 6 HOH H 59 461 62 HOH HOH . G 6 HOH H 60 462 63 HOH HOH . G 6 HOH H 61 463 65 HOH HOH . G 6 HOH H 62 464 66 HOH HOH . G 6 HOH H 63 465 67 HOH HOH . G 6 HOH H 64 466 68 HOH HOH . G 6 HOH H 65 467 69 HOH HOH . G 6 HOH H 66 468 70 HOH HOH . G 6 HOH H 67 469 71 HOH HOH . G 6 HOH H 68 470 72 HOH HOH . G 6 HOH H 69 471 73 HOH HOH . G 6 HOH H 70 472 74 HOH HOH . G 6 HOH H 71 473 75 HOH HOH . G 6 HOH H 72 474 76 HOH HOH . G 6 HOH H 73 475 77 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 C C1 SN3 . . . E 5 20.655 -15.222 18.446 1 48.69 ? C1 SN3 401 H 1 HETATM 2 C C2 SN3 . . . E 5 21.176 -14.095 19.376 1 46.56 ? C2 SN3 401 H 1 HETATM 3 C C3 SN3 . . . E 5 20.219 -13.557 20.437 1 43.85 ? C3 SN3 401 H 1 HETATM 4 C C4 SN3 . . . E 5 19.184 -14.565 20.969 1 45.17 ? C4 SN3 401 H 1 HETATM 5 C C5 SN3 . . . E 5 18.611 -15.545 19.914 1 46.82 ? C5 SN3 401 H 1 HETATM 6 C C6 SN3 . . . E 5 19.753 -16.255 19.181 1 48.66 ? C6 SN3 401 H 1 HETATM 7 O O7 SN3 . . . E 5 20.482 -17.049 20.139 1 48.99 ? O7 SN3 401 H 1 HETATM 8 N N8 SN3 . . . E 5 18.155 -13.668 21.558 1 44.25 ? N8 SN3 401 H 1 HETATM 9 C C9 SN3 . . . E 5 18.19 -12.379 20.864 1 44.8 ? C9 SN3 401 H 1 HETATM 10 C C10 SN3 . . . E 5 19.318 -12.473 19.817 1 43.83 ? C10 SN3 401 H 1 HETATM 11 C C11 SN3 . . . E 5 16.878 -12.13 20.153 1 47.22 ? C11 SN3 401 H 1 HETATM 12 N N12 SN3 . . . E 5 16.365 -10.872 20.154 1 43.83 ? N12 SN3 401 H 1 HETATM 13 C C13 SN3 . . . E 5 15.098 -10.602 19.449 1 42.43 ? C13 SN3 401 H 1 HETATM 14 C C14 SN3 . . . E 5 14.281 -9.611 20.27 1 39.35 ? C14 SN3 401 H 1 HETATM 15 C C15 SN3 . . . E 5 13.558 -10.383 21.348 1 36.86 ? C15 SN3 401 H 1 HETATM 16 C C16 SN3 . . . E 5 12.961 -9.731 22.55 1 36.3 ? C16 SN3 401 H 1 HETATM 17 N N17 SN3 . . . E 5 12.209 -10.755 23.271 1 35.18 ? N17 SN3 401 H 1 HETATM 18 C C18 SN3 . . . E 5 12.607 -12.034 22.67 1 35.65 ? C18 SN3 401 H 1 HETATM 19 C C19 SN3 . . . E 5 13.388 -11.683 21.422 1 35.73 ? C19 SN3 401 H 1 HETATM 20 C C20 SN3 . . . E 5 11.347 -10.539 24.238 1 39.66 ? C20 SN3 401 H 1 HETATM 21 N N21 SN3 . . . E 5 10.664 -11.592 24.821 1 40.21 ? N21 SN3 401 H 1 HETATM 22 N N22 SN3 . . . E 5 11.086 -9.263 24.653 1 35.74 ? N22 SN3 401 H 1 HETATM 23 O O23 SN3 . . . E 5 16.305 -13.056 19.582 1 46.15 ? O23 SN3 401 H 1 HETATM 24 C C24 SN3 . . . E 5 17.332 -13.971 22.58 1 44.85 ? C24 SN3 401 H 1 HETATM 25 O O25 SN3 . . . E 5 16.56 -13.112 22.946 1 40.89 ? O25 SN3 401 H 1 HETATM 26 C C26 SN3 . . . E 5 17.366 -15.327 23.271 1 46 ? C26 SN3 401 H 1 HETATM 27 C C27 SN3 . . . E 5 17.745 -15.115 24.75 1 45.37 ? C27 SN3 401 H 1 HETATM 28 C C28 SN3 . . . E 5 17.741 -16.408 25.571 1 45.34 ? C28 SN3 401 H 1 HETATM 29 C C29 SN3 . . . E 5 18.658 -17.501 24.992 1 45.47 ? C29 SN3 401 H 1 HETATM 30 C C30 SN3 . . . E 5 18.158 -16.049 26.995 1 44.63 ? C30 SN3 401 H 1 HETATM 31 CL CL31 SN3 . . . E 5 19.334 -14.269 24.819 1 47.3 ? CL31 SN3 401 H 1 HETATM 32 N N32 SN3 . . . E 5 16.043 -15.948 23.241 1 50.01 ? N32 SN3 401 H 1 HETATM 33 C C33 SN3 . . . E 5 15.769 -17.033 22.477 1 52.39 ? C33 SN3 401 H 1 HETATM 34 C C34 SN3 . . . E 5 14.389 -17.615 22.522 1 52.31 ? C34 SN3 401 H 1 HETATM 35 O O35 SN3 . . . E 5 13.451 -16.603 22.925 1 51.2 ? O35 SN3 401 H 1 HETATM 36 C C36 SN3 . . . E 5 12.928 -15.839 21.824 1 49.5 ? C36 SN3 401 H 1 HETATM 37 C C37 SN3 . . . E 5 14.411 -18.827 23.471 1 54.41 ? C37 SN3 401 H 1 HETATM 38 O O38 SN3 . . . E 5 14.486 -18.467 24.862 1 58.54 ? O38 SN3 401 H 1 HETATM 39 S S39 SN3 . . . E 5 15.053 -19.563 25.796 1 61.3 ? S39 SN3 401 H 1 HETATM 40 O O40 SN3 . . . E 5 15.221 -19.01 27.092 1 60.47 ? O40 SN3 401 H 1 HETATM 41 O O41 SN3 . . . E 5 13.975 -20.62 26.032 1 60.89 ? O41 SN3 401 H 1 HETATM 42 O O42 SN3 . . . E 5 16.113 -20.172 25.054 1 59.32 ? O42 SN3 401 H 1 HETATM 43 O O43 SN3 . . . E 5 16.601 -17.548 21.75 1 54.45 ? O43 SN3 401 H 1 HETATM 44 O O46 SN3 . . . E 5 19.994 -14.632 17.31 1 49.79 ? O46 SN3 401 H 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 44 #