data_2GN6 # _model_server_result.job_id 1FXeeEBGmRfmGJbKWCQrOg _model_server_result.datetime_utc '2024-12-21 14:33:51' _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 2gn6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":335}' # _entry.id 2GN6 # _exptl.entry_id 2GN6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 607.354 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _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 120 _cell.entry_id 2GN6 _cell.length_a 109.846 _cell.length_b 109.846 _cell.length_c 107.978 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GN6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS hexameric 6 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1,2,3 B,E,F,G,I 2 1 A,C,D,H 2 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 54.923 95.129427 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -54.923 95.129427 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 # _chem_comp.formula 'C17 H27 N3 O17 P2' _chem_comp.formula_weight 607.354 _chem_comp.id UD1 _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _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 C1' C2' UD1 sing 463 n n C1' O1' UD1 sing 464 n n C1' O5' UD1 sing 465 n n C1' H1' UD1 sing 466 n n C2' C3' UD1 sing 467 n n C2' N2' UD1 sing 468 n n C2' H2' UD1 sing 469 n n C3' C4' UD1 sing 470 n n C3' O3' UD1 sing 471 n n C3' H3' UD1 sing 472 n n C4' C5' UD1 sing 473 n n C4' O4' UD1 sing 474 n n C4' H4' UD1 sing 475 n n C5' C6' UD1 sing 476 n n C5' O5' UD1 sing 477 n n C5' H5' UD1 sing 478 n n C6' O6' UD1 sing 479 n n C6' "H6'1" UD1 sing 480 n n C6' "H6'2" UD1 sing 481 n n C7' C8' UD1 sing 482 n n C7' N2' UD1 sing 483 n n C7' O7' UD1 doub 484 n n C8' "H8'1" UD1 sing 485 n n C8' "H8'2" UD1 sing 486 n n C8' "H8'3" UD1 sing 487 n n N2' HN2' UD1 sing 488 n n O1' PB UD1 sing 489 n n O3' HO3' UD1 sing 490 n n O4' HO4' UD1 sing 491 n n O6' HO6' UD1 sing 492 n n N1 C2 UD1 sing 493 n n N1 C6 UD1 sing 494 n n N1 C1B UD1 sing 495 n n C2 N3 UD1 sing 496 n n C2 O2 UD1 doub 497 n n N3 C4 UD1 sing 498 n n N3 HN3 UD1 sing 499 n n C4 C5 UD1 sing 500 n n C4 O4 UD1 doub 501 n n C5 C6 UD1 doub 502 n n C5 H5 UD1 sing 503 n n C6 H6 UD1 sing 504 n n C1B C2B UD1 sing 505 n n C1B O4B UD1 sing 506 n n C1B H1B UD1 sing 507 n n C2B O2' UD1 sing 508 n n C2B C3B UD1 sing 509 n n C2B H2B UD1 sing 510 n n O2' HO2' UD1 sing 511 n n C3B C4B UD1 sing 512 n n C3B O3B UD1 sing 513 n n C3B H3B UD1 sing 514 n n C4B O4B UD1 sing 515 n n C4B C5B UD1 sing 516 n n C4B H4B UD1 sing 517 n n O3B HO3A UD1 sing 518 n n C5B O5B UD1 sing 519 n n C5B "H5'1" UD1 sing 520 n n C5B "H5'2" UD1 sing 521 n n O5B PA UD1 sing 522 n n PA O1A UD1 doub 523 n n PA O2A UD1 sing 524 n n PA O3A UD1 sing 525 n n O2A HOA2 UD1 sing 526 n n O3A PB UD1 sing 527 n n PB O1B UD1 doub 528 n n PB O2B UD1 sing 529 n n O2B HOB2 UD1 sing 530 n n # _atom_sites.entry_id 2GN6 _atom_sites.fract_transf_matrix[1][1] 0.009104 _atom_sites.fract_transf_matrix[1][2] 0.005256 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010512 _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] 0.009261 _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 NAP A 1 334 334 NAP NAP . D 3 UD1 A 1 335 335 UD1 UD1 . E 2 NAP B 1 334 334 NAP NAP . F 3 UD1 B 1 335 335 UD1 UD1 . G 4 MES B 1 336 336 MES MES . H 5 HOH A 1 336 10 HOH HOH . H 5 HOH A 2 337 13 HOH HOH . H 5 HOH A 3 338 15 HOH HOH . H 5 HOH A 4 339 19 HOH HOH . H 5 HOH A 5 340 21 HOH HOH . H 5 HOH A 6 341 22 HOH HOH . H 5 HOH A 7 342 23 HOH HOH . H 5 HOH A 8 343 24 HOH HOH . H 5 HOH A 9 344 26 HOH HOH . H 5 HOH A 10 345 28 HOH HOH . H 5 HOH A 11 346 29 HOH HOH . H 5 HOH A 12 347 30 HOH HOH . H 5 HOH A 13 348 31 HOH HOH . H 5 HOH A 14 349 33 HOH HOH . H 5 HOH A 15 350 36 HOH HOH . H 5 HOH A 16 351 38 HOH HOH . H 5 HOH A 17 352 40 HOH HOH . H 5 HOH A 18 353 45 HOH HOH . H 5 HOH A 19 354 48 HOH HOH . H 5 HOH A 20 355 53 HOH HOH . H 5 HOH A 21 356 54 HOH HOH . H 5 HOH A 22 357 55 HOH HOH . H 5 HOH A 23 358 57 HOH HOH . H 5 HOH A 24 359 58 HOH HOH . H 5 HOH A 25 360 59 HOH HOH . H 5 HOH A 26 361 60 HOH HOH . H 5 HOH A 27 362 63 HOH HOH . H 5 HOH A 28 363 64 HOH HOH . H 5 HOH A 29 364 67 HOH HOH . H 5 HOH A 30 365 70 HOH HOH . H 5 HOH A 31 366 74 HOH HOH . H 5 HOH A 32 367 75 HOH HOH . H 5 HOH A 33 368 78 HOH HOH . H 5 HOH A 34 369 79 HOH HOH . H 5 HOH A 35 370 80 HOH HOH . H 5 HOH A 36 371 85 HOH HOH . H 5 HOH A 37 372 87 HOH HOH . H 5 HOH A 38 373 88 HOH HOH . H 5 HOH A 39 374 89 HOH HOH . H 5 HOH A 40 375 91 HOH HOH . H 5 HOH A 41 376 95 HOH HOH . H 5 HOH A 42 377 98 HOH HOH . H 5 HOH A 43 378 99 HOH HOH . H 5 HOH A 44 379 100 HOH HOH . H 5 HOH A 45 380 101 HOH HOH . H 5 HOH A 46 381 106 HOH HOH . H 5 HOH A 47 382 108 HOH HOH . H 5 HOH A 48 383 109 HOH HOH . H 5 HOH A 49 384 110 HOH HOH . H 5 HOH A 50 385 111 HOH HOH . H 5 HOH A 51 386 115 HOH HOH . H 5 HOH A 52 387 116 HOH HOH . H 5 HOH A 53 388 118 HOH HOH . H 5 HOH A 54 389 119 HOH HOH . H 5 HOH A 55 390 120 HOH HOH . H 5 HOH A 56 391 121 HOH HOH . H 5 HOH A 57 392 122 HOH HOH . H 5 HOH A 58 393 123 HOH HOH . H 5 HOH A 59 394 128 HOH HOH . H 5 HOH A 60 395 129 HOH HOH . H 5 HOH A 61 396 132 HOH HOH . H 5 HOH A 62 397 136 HOH HOH . H 5 HOH A 63 398 137 HOH HOH . H 5 HOH A 64 399 139 HOH HOH . H 5 HOH A 65 400 140 HOH HOH . H 5 HOH A 66 401 149 HOH HOH . H 5 HOH A 67 402 150 HOH HOH . H 5 HOH A 68 403 152 HOH HOH . H 5 HOH A 69 404 153 HOH HOH . H 5 HOH A 70 405 155 HOH HOH . H 5 HOH A 71 406 156 HOH HOH . H 5 HOH A 72 407 157 HOH HOH . H 5 HOH A 73 408 158 HOH HOH . H 5 HOH A 74 409 163 HOH HOH . H 5 HOH A 75 410 164 HOH HOH . H 5 HOH A 76 411 165 HOH HOH . H 5 HOH A 77 412 167 HOH HOH . I 5 HOH B 1 337 1 HOH HOH . I 5 HOH B 2 338 2 HOH HOH . I 5 HOH B 3 339 3 HOH HOH . I 5 HOH B 4 340 4 HOH HOH . I 5 HOH B 5 341 5 HOH HOH . I 5 HOH B 6 342 6 HOH HOH . I 5 HOH B 7 343 7 HOH HOH . I 5 HOH B 8 344 8 HOH HOH . I 5 HOH B 9 345 9 HOH HOH . I 5 HOH B 10 346 11 HOH HOH . I 5 HOH B 11 347 12 HOH HOH . I 5 HOH B 12 348 14 HOH HOH . I 5 HOH B 13 349 16 HOH HOH . I 5 HOH B 14 350 17 HOH HOH . I 5 HOH B 15 351 18 HOH HOH . I 5 HOH B 16 352 20 HOH HOH . I 5 HOH B 17 353 25 HOH HOH . I 5 HOH B 18 354 27 HOH HOH . I 5 HOH B 19 355 32 HOH HOH . I 5 HOH B 20 356 34 HOH HOH . I 5 HOH B 21 357 35 HOH HOH . I 5 HOH B 22 358 37 HOH HOH . I 5 HOH B 23 359 39 HOH HOH . I 5 HOH B 24 360 41 HOH HOH . I 5 HOH B 25 361 42 HOH HOH . I 5 HOH B 26 362 43 HOH HOH . I 5 HOH B 27 363 44 HOH HOH . I 5 HOH B 28 364 46 HOH HOH . I 5 HOH B 29 365 47 HOH HOH . I 5 HOH B 30 366 49 HOH HOH . I 5 HOH B 31 367 50 HOH HOH . I 5 HOH B 32 368 51 HOH HOH . I 5 HOH B 33 369 52 HOH HOH . I 5 HOH B 34 370 56 HOH HOH . I 5 HOH B 35 371 61 HOH HOH . I 5 HOH B 36 372 62 HOH HOH . I 5 HOH B 37 373 65 HOH HOH . I 5 HOH B 38 374 66 HOH HOH . I 5 HOH B 39 375 68 HOH HOH . I 5 HOH B 40 376 69 HOH HOH . I 5 HOH B 41 377 71 HOH HOH . I 5 HOH B 42 378 72 HOH HOH . I 5 HOH B 43 379 73 HOH HOH . I 5 HOH B 44 380 76 HOH HOH . I 5 HOH B 45 381 77 HOH HOH . I 5 HOH B 46 382 81 HOH HOH . I 5 HOH B 47 383 82 HOH HOH . I 5 HOH B 48 384 83 HOH HOH . I 5 HOH B 49 385 84 HOH HOH . I 5 HOH B 50 386 86 HOH HOH . I 5 HOH B 51 387 90 HOH HOH . I 5 HOH B 52 388 92 HOH HOH . I 5 HOH B 53 389 93 HOH HOH . I 5 HOH B 54 390 94 HOH HOH . I 5 HOH B 55 391 96 HOH HOH . I 5 HOH B 56 392 97 HOH HOH . I 5 HOH B 57 393 102 HOH HOH . I 5 HOH B 58 394 103 HOH HOH . I 5 HOH B 59 395 104 HOH HOH . I 5 HOH B 60 396 105 HOH HOH . I 5 HOH B 61 397 107 HOH HOH . I 5 HOH B 62 398 112 HOH HOH . I 5 HOH B 63 399 113 HOH HOH . I 5 HOH B 64 400 114 HOH HOH . I 5 HOH B 65 401 117 HOH HOH . I 5 HOH B 66 402 124 HOH HOH . I 5 HOH B 67 403 125 HOH HOH . I 5 HOH B 68 404 126 HOH HOH . I 5 HOH B 69 405 127 HOH HOH . I 5 HOH B 70 406 130 HOH HOH . I 5 HOH B 71 407 131 HOH HOH . I 5 HOH B 72 408 133 HOH HOH . I 5 HOH B 73 409 134 HOH HOH . I 5 HOH B 74 410 135 HOH HOH . I 5 HOH B 75 411 138 HOH HOH . I 5 HOH B 76 412 141 HOH HOH . I 5 HOH B 77 413 142 HOH HOH . I 5 HOH B 78 414 143 HOH HOH . I 5 HOH B 79 415 144 HOH HOH . I 5 HOH B 80 416 145 HOH HOH . I 5 HOH B 81 417 146 HOH HOH . I 5 HOH B 82 418 147 HOH HOH . I 5 HOH B 83 419 148 HOH HOH . I 5 HOH B 84 420 151 HOH HOH . I 5 HOH B 85 421 154 HOH HOH . I 5 HOH B 86 422 159 HOH HOH . I 5 HOH B 87 423 160 HOH HOH . I 5 HOH B 88 424 161 HOH HOH . I 5 HOH B 89 425 162 HOH HOH . I 5 HOH B 90 426 166 HOH HOH . I 5 HOH B 91 427 168 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' UD1 . . . F 3 33.263 56.726 2.894 0 70.57 ? C1' UD1 335 B 1 HETATM 2 C C2' UD1 . . . F 3 31.768 56.468 3.026 0 71.53 ? C2' UD1 335 B 1 HETATM 3 C C3' UD1 . . . F 3 31.043 57.714 3.52 0 71.93 ? C3' UD1 335 B 1 HETATM 4 C C4' UD1 . . . F 3 31.725 58.283 4.752 0 72.03 ? C4' UD1 335 B 1 HETATM 5 C C5' UD1 . . . F 3 33.194 58.539 4.438 0 71.92 ? C5' UD1 335 B 1 HETATM 6 C C6' UD1 . . . F 3 33.904 59.099 5.645 0 72.18 ? C6' UD1 335 B 1 HETATM 7 C C7' UD1 . . . F 3 30.75 54.764 1.59 0 72.65 ? C7' UD1 335 B 1 HETATM 8 C C8' UD1 . . . F 3 31.673 53.843 0.827 0 72.89 ? C8' UD1 335 B 1 HETATM 9 N N2' UD1 . . . F 3 31.218 56.049 1.731 0 72.21 ? N2' UD1 335 B 1 HETATM 10 O O1' UD1 . . . F 3 33.509 57.728 1.912 1 68.47 ? O1' UD1 335 B 1 HETATM 11 O O3' UD1 . . . F 3 29.721 57.347 3.874 0 72.12 ? O3' UD1 335 B 1 HETATM 12 O O4' UD1 . . . F 3 31.098 59.521 5.068 0 72.26 ? O4' UD1 335 B 1 HETATM 13 O O5' UD1 . . . F 3 33.831 57.305 4.083 0 71.26 ? O5' UD1 335 B 1 HETATM 14 O O6' UD1 . . . F 3 34.713 60.179 5.207 0 72.5 ? O6' UD1 335 B 1 HETATM 15 O O7' UD1 . . . F 3 29.686 54.4 2.032 0 72.89 ? O7' UD1 335 B 1 HETATM 16 N N1 UD1 . . . F 3 40.014 54.739 -2.883 1 60.33 ? N1 UD1 335 B 1 HETATM 17 C C2 UD1 . . . F 3 41.011 54.223 -3.709 1 59.2 ? C2 UD1 335 B 1 HETATM 18 N N3 UD1 . . . F 3 40.637 53.224 -4.6 1 58.08 ? N3 UD1 335 B 1 HETATM 19 C C4 UD1 . . . F 3 39.352 52.69 -4.74 1 59.63 ? C4 UD1 335 B 1 HETATM 20 C C5 UD1 . . . F 3 38.325 53.282 -3.823 1 60.26 ? C5 UD1 335 B 1 HETATM 21 C C6 UD1 . . . F 3 38.726 54.259 -2.962 1 61.12 ? C6 UD1 335 B 1 HETATM 22 O O2 UD1 . . . F 3 42.161 54.622 -3.663 1 57.54 ? O2 UD1 335 B 1 HETATM 23 O O4 UD1 . . . F 3 39.087 51.808 -5.546 1 58.71 ? O4 UD1 335 B 1 HETATM 24 C C1B UD1 . . . F 3 40.365 55.807 -1.916 1 60.52 ? C1B UD1 335 B 1 HETATM 25 C C2B UD1 . . . F 3 39.518 57.044 -2.064 1 60.57 ? C2B UD1 335 B 1 HETATM 26 O O2' UD1 . . . F 3 40.172 57.969 -2.923 1 61.1 ? O2' UD1 335 B 1 HETATM 27 C C3B UD1 . . . F 3 39.356 57.596 -0.689 1 59.86 ? C3B UD1 335 B 1 HETATM 28 C C4B UD1 . . . F 3 39.688 56.448 0.232 1 59.59 ? C4B UD1 335 B 1 HETATM 29 O O4B UD1 . . . F 3 40.21 55.371 -0.56 1 60.66 ? O4B UD1 335 B 1 HETATM 30 O O3B UD1 . . . F 3 40.313 58.623 -0.461 1 56.42 ? O3B UD1 335 B 1 HETATM 31 C C5B UD1 . . . F 3 38.449 55.965 0.959 1 58.71 ? C5B UD1 335 B 1 HETATM 32 O O5B UD1 . . . F 3 37.509 55.544 -0.003 1 58.79 ? O5B UD1 335 B 1 HETATM 33 P PA UD1 . . . F 3 36.091 55.002 0.543 1 61.88 ? PA UD1 335 B 1 HETATM 34 O O1A UD1 . . . F 3 35.069 54.505 -0.607 1 59.4 ? O1A UD1 335 B 1 HETATM 35 O O2A UD1 . . . F 3 36.503 53.865 1.623 1 62.63 ? O2A UD1 335 B 1 HETATM 36 O O3A UD1 . . . F 3 35.53 56.201 1.456 1 64.63 ? O3A UD1 335 B 1 HETATM 37 P PB UD1 . . . F 3 34.868 57.608 1.032 1 65.98 ? PB UD1 335 B 1 HETATM 38 O O1B UD1 . . . F 3 34.64 57.784 -0.561 1 66.92 ? O1B UD1 335 B 1 HETATM 39 O O2B UD1 . . . F 3 35.862 58.698 1.698 1 64.87 ? O2B UD1 335 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #