data_3GSM # _model_server_result.job_id P6i1KBf0sYLGFmZit_dKHw _model_server_result.datetime_utc '2024-11-09 23:21:24' _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 3gsm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":341}' # _entry.id 3GSM # _exptl.entry_id 3GSM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 395.407 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(pentanoylamino)oxan-2-ylidene]amino] N-phenylcarbamate' _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 90 _cell.entry_id 3GSM _cell.length_a 47.98 _cell.length_b 86.44 _cell.length_c 86.44 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GSM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C18 H25 N3 O7' _chem_comp.formula_weight 395.407 _chem_comp.id VPU _chem_comp.mon_nstd_flag . _chem_comp.name '[[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(pentanoylamino)oxan-2-ylidene]amino] N-phenylcarbamate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-Valeryl-PUGNAc # 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 C3 C2 VPU sing 389 n n C2 C1 VPU sing 390 n n C1 CAH VPU sing 391 n n CAH CAG VPU sing 392 n n CAG OAN VPU doub 393 n n CAG NAI VPU sing 394 n n NAI CAB VPU sing 395 n n CAB CAC VPU sing 396 n n CAB CAA VPU sing 397 n n CAC OAJ VPU sing 398 n n CAC CAD VPU sing 399 n n CAD OAK VPU sing 400 n n CAD CAE VPU sing 401 n n CAE CAF VPU sing 402 n n CAE OAL VPU sing 403 n n CAF OAM VPU sing 404 n n OAL CAA VPU sing 405 n n CAA NAY VPU doub 406 n n NAY OAQ VPU sing 407 n n OAQ CAP VPU sing 408 n n CAP OAR VPU doub 409 n n CAP NAO VPU sing 410 n n NAO CAS VPU sing 411 n n CAS CAT VPU doub 412 n y CAS CAX VPU sing 413 n y CAT CAU VPU sing 414 n y CAU CAV VPU doub 415 n y CAV CAW VPU sing 416 n y CAW CAX VPU doub 417 n y C3 H3 VPU sing 418 n n C3 H3A VPU sing 419 n n C3 H3B VPU sing 420 n n C2 H2 VPU sing 421 n n C2 H2A VPU sing 422 n n C1 H1 VPU sing 423 n n C1 H1A VPU sing 424 n n CAH HAH VPU sing 425 z n CAH HAHA VPU sing 426 n n NAI HNAI VPU sing 427 n n CAB HAB VPU sing 428 n n CAC HAC VPU sing 429 n n OAJ HOAJ VPU sing 430 n n CAD HAD VPU sing 431 n n OAK HOAK VPU sing 432 n n CAE HAE VPU sing 433 n n CAF HAF VPU sing 434 n n CAF HAFA VPU sing 435 n n OAM HOAM VPU sing 436 n n NAO HNAO VPU sing 437 n n CAT HAT VPU sing 438 n n CAU HAU VPU sing 439 n n CAV HAV VPU sing 440 n n CAW HAW VPU sing 441 n n CAX HAX VPU sing 442 n n # _atom_sites.entry_id 3GSM _atom_sites.fract_transf_matrix[1][1] 0.020842 _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] 0.011569 _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] 0.011569 _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 VPU A 1 341 341 VPU VPU . C 3 GOL A 1 343 343 GOL GOL . D 3 GOL A 1 344 344 GOL GOL . E 4 HOH A 1 345 345 HOH HOH . E 4 HOH A 2 346 346 HOH HOH . E 4 HOH A 3 347 347 HOH HOH . E 4 HOH A 4 348 348 HOH HOH . E 4 HOH A 5 349 349 HOH HOH . E 4 HOH A 6 350 350 HOH HOH . E 4 HOH A 7 351 351 HOH HOH . E 4 HOH A 8 352 352 HOH HOH . E 4 HOH A 9 353 353 HOH HOH . E 4 HOH A 10 354 354 HOH HOH . E 4 HOH A 11 355 355 HOH HOH . E 4 HOH A 12 356 356 HOH HOH . E 4 HOH A 13 357 357 HOH HOH . E 4 HOH A 14 358 358 HOH HOH . E 4 HOH A 15 359 359 HOH HOH . E 4 HOH A 16 360 360 HOH HOH . E 4 HOH A 17 361 361 HOH HOH . E 4 HOH A 18 362 362 HOH HOH . E 4 HOH A 19 363 363 HOH HOH . E 4 HOH A 20 364 364 HOH HOH . E 4 HOH A 21 365 365 HOH HOH . E 4 HOH A 22 366 366 HOH HOH . E 4 HOH A 23 367 367 HOH HOH . E 4 HOH A 24 368 368 HOH HOH . E 4 HOH A 25 369 369 HOH HOH . E 4 HOH A 26 370 370 HOH HOH . E 4 HOH A 27 371 371 HOH HOH . E 4 HOH A 28 372 372 HOH HOH . E 4 HOH A 29 373 373 HOH HOH . E 4 HOH A 30 374 374 HOH HOH . E 4 HOH A 31 375 375 HOH HOH . E 4 HOH A 32 376 376 HOH HOH . E 4 HOH A 33 377 377 HOH HOH . E 4 HOH A 34 378 378 HOH HOH . E 4 HOH A 35 379 379 HOH HOH . E 4 HOH A 36 380 380 HOH HOH . E 4 HOH A 37 381 381 HOH HOH . E 4 HOH A 38 382 382 HOH HOH . E 4 HOH A 39 383 383 HOH HOH . E 4 HOH A 40 384 384 HOH HOH . E 4 HOH A 41 385 385 HOH HOH . E 4 HOH A 42 386 386 HOH HOH . E 4 HOH A 43 387 387 HOH HOH . E 4 HOH A 44 388 388 HOH HOH . E 4 HOH A 45 389 389 HOH HOH . E 4 HOH A 46 390 390 HOH HOH . E 4 HOH A 47 391 391 HOH HOH . E 4 HOH A 48 392 392 HOH HOH . E 4 HOH A 49 393 393 HOH HOH . E 4 HOH A 50 394 394 HOH HOH . E 4 HOH A 51 395 395 HOH HOH . E 4 HOH A 52 396 396 HOH HOH . E 4 HOH A 53 397 397 HOH HOH . E 4 HOH A 54 398 398 HOH HOH . E 4 HOH A 55 399 399 HOH HOH . E 4 HOH A 56 400 400 HOH HOH . E 4 HOH A 57 401 401 HOH HOH . E 4 HOH A 58 402 402 HOH HOH . E 4 HOH A 59 403 403 HOH HOH . E 4 HOH A 60 404 404 HOH HOH . E 4 HOH A 61 405 405 HOH HOH . E 4 HOH A 62 406 406 HOH HOH . E 4 HOH A 63 407 407 HOH HOH . E 4 HOH A 64 408 408 HOH HOH . E 4 HOH A 65 409 409 HOH HOH . E 4 HOH A 66 410 410 HOH HOH . E 4 HOH A 67 411 411 HOH HOH . E 4 HOH A 68 412 412 HOH HOH . E 4 HOH A 69 413 413 HOH HOH . E 4 HOH A 70 414 414 HOH HOH . E 4 HOH A 71 415 415 HOH HOH . E 4 HOH A 72 416 416 HOH HOH . E 4 HOH A 73 417 417 HOH HOH . E 4 HOH A 74 418 418 HOH HOH . E 4 HOH A 75 419 419 HOH HOH . E 4 HOH A 76 420 420 HOH HOH . E 4 HOH A 77 421 421 HOH HOH . E 4 HOH A 78 422 422 HOH HOH . E 4 HOH A 79 423 423 HOH HOH . E 4 HOH A 80 424 424 HOH HOH . E 4 HOH A 81 425 425 HOH HOH . E 4 HOH A 82 426 426 HOH HOH . E 4 HOH A 83 427 427 HOH HOH . E 4 HOH A 84 428 428 HOH HOH . E 4 HOH A 85 429 429 HOH HOH . E 4 HOH A 86 430 430 HOH HOH . E 4 HOH A 87 431 431 HOH HOH . E 4 HOH A 88 432 432 HOH HOH . E 4 HOH A 89 433 433 HOH HOH . E 4 HOH A 90 434 434 HOH HOH . E 4 HOH A 91 435 435 HOH HOH . E 4 HOH A 92 436 436 HOH HOH . E 4 HOH A 93 437 437 HOH HOH . E 4 HOH A 94 438 438 HOH HOH . E 4 HOH A 95 439 439 HOH HOH . E 4 HOH A 96 440 440 HOH HOH . E 4 HOH A 97 441 441 HOH HOH . E 4 HOH A 98 442 442 HOH HOH . E 4 HOH A 99 443 443 HOH HOH . E 4 HOH A 100 444 444 HOH HOH . E 4 HOH A 101 445 445 HOH HOH . E 4 HOH A 102 446 446 HOH HOH . E 4 HOH A 103 447 447 HOH HOH . E 4 HOH A 104 448 448 HOH HOH . E 4 HOH A 105 449 449 HOH HOH . E 4 HOH A 106 450 450 HOH HOH . E 4 HOH A 107 451 451 HOH HOH . E 4 HOH A 108 452 452 HOH HOH . E 4 HOH A 109 453 453 HOH HOH . E 4 HOH A 110 454 454 HOH HOH . E 4 HOH A 111 455 455 HOH HOH . E 4 HOH A 112 456 456 HOH HOH . E 4 HOH A 113 457 457 HOH HOH . E 4 HOH A 114 458 458 HOH HOH . E 4 HOH A 115 459 459 HOH HOH . E 4 HOH A 116 460 460 HOH HOH . E 4 HOH A 117 461 461 HOH HOH . E 4 HOH A 118 462 462 HOH HOH . E 4 HOH A 119 463 463 HOH HOH . E 4 HOH A 120 464 464 HOH HOH . E 4 HOH A 121 465 465 HOH HOH . E 4 HOH A 122 466 466 HOH HOH . E 4 HOH A 123 467 467 HOH HOH . E 4 HOH A 124 468 468 HOH HOH . E 4 HOH A 125 469 469 HOH HOH . E 4 HOH A 126 470 470 HOH HOH . E 4 HOH A 127 471 471 HOH HOH . E 4 HOH A 128 472 472 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 C3 VPU . . . B 2 -8.571 18.593 12.453 1 82.35 ? C3 VPU 341 A 1 HETATM 2 C C2 VPU . . . B 2 -7.654 18.62 13.688 1 82.89 ? C2 VPU 341 A 1 HETATM 3 C C1 VPU . . . B 2 -7.518 17.255 14.346 1 82.81 ? C1 VPU 341 A 1 HETATM 4 C CAH VPU . . . B 2 -6.053 16.885 14.605 1 82.79 ? CAH VPU 341 A 1 HETATM 5 C CAG VPU . . . B 2 -5.456 16.226 13.374 1 83.08 ? CAG VPU 341 A 1 HETATM 6 O OAN VPU . . . B 2 -6.113 15.387 12.768 1 82.6 ? OAN VPU 341 A 1 HETATM 7 N NAI VPU . . . B 2 -4.215 16.604 13.008 1 83.73 ? NAI VPU 341 A 1 HETATM 8 C CAB VPU . . . B 2 -3.533 16.05 11.825 1 84.56 ? CAB VPU 341 A 1 HETATM 9 C CAC VPU . . . B 2 -2.577 14.918 12.24 1 84.54 ? CAC VPU 341 A 1 HETATM 10 O OAJ VPU . . . B 2 -3.228 13.842 12.946 1 83.14 ? OAJ VPU 341 A 1 HETATM 11 C CAD VPU . . . B 2 -1.931 14.395 10.952 1 84.87 ? CAD VPU 341 A 1 HETATM 12 O OAK VPU . . . B 2 -1.236 13.158 11.195 1 84.99 ? OAK VPU 341 A 1 HETATM 13 C CAE VPU . . . B 2 -0.971 15.428 10.341 1 84.63 ? CAE VPU 341 A 1 HETATM 14 C CAF VPU . . . B 2 -0.589 15.011 8.93 1 84.3 ? CAF VPU 341 A 1 HETATM 15 O OAM VPU . . . B 2 -1.262 15.37 7.973 1 83.85 ? OAM VPU 341 A 1 HETATM 16 O OAL VPU . . . B 2 -1.507 16.766 10.3 1 84.82 ? OAL VPU 341 A 1 HETATM 17 C CAA VPU . . . B 2 -2.741 17.077 11.032 1 84.69 ? CAA VPU 341 A 1 HETATM 18 N NAY VPU . . . B 2 -3.192 18.258 10.974 1 84.59 ? NAY VPU 341 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #