data_2GN9 # _model_server_result.job_id JvXtglblX5IaKR4CBTmNTw _model_server_result.datetime_utc '2024-12-21 13:53:50' _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 2gn9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":335}' # _entry.id 2GN9 # _exptl.entry_id 2GN9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 2GN9 _cell.length_a 112.376 _cell.length_b 112.376 _cell.length_c 107.349 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GN9 _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 56.188 97.320471 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 -56.188 97.320471 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 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 N1 C2 UPG sing 463 n n N1 C6 UPG sing 464 n n N1 C1C UPG sing 465 n n C2 N3 UPG sing 466 n n C2 O2 UPG doub 467 n n N3 C4 UPG sing 468 n n N3 HN3 UPG sing 469 n n C4 C5 UPG sing 470 n n C4 O4 UPG doub 471 n n C5 C6 UPG doub 472 n n C5 H5 UPG sing 473 n n C6 H6 UPG sing 474 n n C1C C2C UPG sing 475 n n C1C O4C UPG sing 476 n n C1C H1C UPG sing 477 n n C2C O2C UPG sing 478 n n C2C C3C UPG sing 479 n n C2C H2C UPG sing 480 n n O2C HO2C UPG sing 481 n n C3C C4C UPG sing 482 n n C3C O3C UPG sing 483 n n C3C H3C UPG sing 484 n n C4C O4C UPG sing 485 n n C4C C5C UPG sing 486 n n C4C H4C UPG sing 487 n n O3C HO3C UPG sing 488 n n C5C O5C UPG sing 489 n n C5C H5C1 UPG sing 490 n n C5C H5C2 UPG sing 491 n n O5C PA UPG sing 492 n n PA O1A UPG doub 493 n n PA O2A UPG sing 494 n n PA O3A UPG sing 495 n n O2A HOA2 UPG sing 496 n n O3A PB UPG sing 497 n n PB O1B UPG doub 498 n n PB O2B UPG sing 499 n n PB O3B UPG sing 500 n n O2B HOB2 UPG sing 501 n n O3B C1' UPG sing 502 n n C1' C2' UPG sing 503 n n C1' O5' UPG sing 504 n n C1' H1' UPG sing 505 n n C2' C3' UPG sing 506 n n C2' O2' UPG sing 507 n n C2' H2' UPG sing 508 n n C3' C4' UPG sing 509 n n C3' O3' UPG sing 510 n n C3' H3' UPG sing 511 n n C4' C5' UPG sing 512 n n C4' O4' UPG sing 513 n n C4' H4' UPG sing 514 n n C5' C6' UPG sing 515 n n C5' O5' UPG sing 516 n n C5' H5' UPG sing 517 n n C6' O6' UPG sing 518 n n C6' "H6'1" UPG sing 519 n n C6' "H6'2" UPG sing 520 n n O2' HO2' UPG sing 521 n n O3' HO3' UPG sing 522 n n O4' HO4' UPG sing 523 n n O6' HO6' UPG sing 524 n n # _atom_sites.entry_id 2GN9 _atom_sites.fract_transf_matrix[1][1] 0.008899 _atom_sites.fract_transf_matrix[1][2] 0.005138 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010275 _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] 0.009315 _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 UPG A 1 335 335 UPG UPG . E 2 NAP B 1 334 334 NAP NAP . F 3 UPG B 1 335 335 UPG UPG . G 4 MES B 1 336 336 MES MES . H 5 HOH A 1 336 1 HOH HOH . H 5 HOH A 2 337 2 HOH HOH . H 5 HOH A 3 338 8 HOH HOH . H 5 HOH A 4 339 16 HOH HOH . H 5 HOH A 5 340 17 HOH HOH . H 5 HOH A 6 341 18 HOH HOH . H 5 HOH A 7 342 20 HOH HOH . H 5 HOH A 8 343 22 HOH HOH . H 5 HOH A 9 344 23 HOH HOH . H 5 HOH A 10 345 24 HOH HOH . H 5 HOH A 11 346 25 HOH HOH . H 5 HOH A 12 347 26 HOH HOH . H 5 HOH A 13 348 27 HOH HOH . H 5 HOH A 14 349 31 HOH HOH . H 5 HOH A 15 350 32 HOH HOH . H 5 HOH A 16 351 35 HOH HOH . H 5 HOH A 17 352 36 HOH HOH . H 5 HOH A 18 353 39 HOH HOH . H 5 HOH A 19 354 41 HOH HOH . H 5 HOH A 20 355 44 HOH HOH . H 5 HOH A 21 356 45 HOH HOH . H 5 HOH A 22 357 46 HOH HOH . H 5 HOH A 23 358 48 HOH HOH . H 5 HOH A 24 359 49 HOH HOH . H 5 HOH A 25 360 53 HOH HOH . H 5 HOH A 26 361 56 HOH HOH . H 5 HOH A 27 362 57 HOH HOH . H 5 HOH A 28 363 58 HOH HOH . H 5 HOH A 29 364 59 HOH HOH . H 5 HOH A 30 365 60 HOH HOH . H 5 HOH A 31 366 64 HOH HOH . H 5 HOH A 32 367 66 HOH HOH . H 5 HOH A 33 368 70 HOH HOH . H 5 HOH A 34 369 74 HOH HOH . I 5 HOH B 1 337 3 HOH HOH . I 5 HOH B 2 338 4 HOH HOH . I 5 HOH B 3 339 5 HOH HOH . I 5 HOH B 4 340 6 HOH HOH . I 5 HOH B 5 341 7 HOH HOH . I 5 HOH B 6 342 9 HOH HOH . I 5 HOH B 7 343 10 HOH HOH . I 5 HOH B 8 344 11 HOH HOH . I 5 HOH B 9 345 12 HOH HOH . I 5 HOH B 10 346 13 HOH HOH . I 5 HOH B 11 347 14 HOH HOH . I 5 HOH B 12 348 15 HOH HOH . I 5 HOH B 13 349 19 HOH HOH . I 5 HOH B 14 350 21 HOH HOH . I 5 HOH B 15 351 28 HOH HOH . I 5 HOH B 16 352 29 HOH HOH . I 5 HOH B 17 353 30 HOH HOH . I 5 HOH B 18 354 33 HOH HOH . I 5 HOH B 19 355 34 HOH HOH . I 5 HOH B 20 356 37 HOH HOH . I 5 HOH B 21 357 38 HOH HOH . I 5 HOH B 22 358 40 HOH HOH . I 5 HOH B 23 359 42 HOH HOH . I 5 HOH B 24 360 43 HOH HOH . I 5 HOH B 25 361 47 HOH HOH . I 5 HOH B 26 362 50 HOH HOH . I 5 HOH B 27 363 51 HOH HOH . I 5 HOH B 28 364 52 HOH HOH . I 5 HOH B 29 365 54 HOH HOH . I 5 HOH B 30 366 55 HOH HOH . I 5 HOH B 31 367 61 HOH HOH . I 5 HOH B 32 368 62 HOH HOH . I 5 HOH B 33 369 63 HOH HOH . I 5 HOH B 34 370 65 HOH HOH . I 5 HOH B 35 371 67 HOH HOH . I 5 HOH B 36 372 68 HOH HOH . I 5 HOH B 37 373 69 HOH HOH . I 5 HOH B 38 374 71 HOH HOH . I 5 HOH B 39 375 72 HOH HOH . I 5 HOH B 40 376 73 HOH HOH . I 5 HOH B 41 377 75 HOH HOH . I 5 HOH B 42 378 76 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 UPG . . . D 3 12.036 26.066 8.255 1 79.98 ? N1 UPG 335 A 1 HETATM 2 C C2 UPG . . . D 3 12.855 25.283 9.066 1 79.27 ? C2 UPG 335 A 1 HETATM 3 N N3 UPG . . . D 3 13.728 25.95 9.91 1 80 ? N3 UPG 335 A 1 HETATM 4 C C4 UPG . . . D 3 13.857 27.338 10.017 1 80 ? C4 UPG 335 A 1 HETATM 5 C C5 UPG . . . D 3 12.948 28.124 9.122 1 80 ? C5 UPG 335 A 1 HETATM 6 C C6 UPG . . . D 3 12.106 27.438 8.309 1 80 ? C6 UPG 335 A 1 HETATM 7 O O2 UPG . . . D 3 12.817 24.069 9.046 1 79.56 ? O2 UPG 335 A 1 HETATM 8 O O4 UPG . . . D 3 14.651 27.868 10.782 1 80 ? O4 UPG 335 A 1 HETATM 9 C C1C UPG . . . D 3 11.104 25.392 7.323 1 80 ? C1C UPG 335 A 1 HETATM 10 C C2C UPG . . . D 3 9.708 25.972 7.314 1 80 ? C2C UPG 335 A 1 HETATM 11 O O2C UPG . . . D 3 8.842 25.086 8.02 1 78.56 ? O2C UPG 335 A 1 HETATM 12 C C3C UPG . . . D 3 9.302 26.082 5.884 1 77.56 ? C3C UPG 335 A 1 HETATM 13 C C4C UPG . . . D 3 10.556 25.836 5.088 1 79.29 ? C4C UPG 335 A 1 HETATM 14 O O4C UPG . . . D 3 11.606 25.456 5.983 1 80 ? O4C UPG 335 A 1 HETATM 15 O O3C UPG . . . D 3 8.38 25.046 5.569 1 73.2 ? O3C UPG 335 A 1 HETATM 16 C C5C UPG . . . D 3 10.976 27.085 4.326 1 78.81 ? C5C UPG 335 A 1 HETATM 17 O O5C UPG . . . D 3 11.506 28.037 5.234 1 78.53 ? O5C UPG 335 A 1 HETATM 18 P PA UPG . . . D 3 11.666 29.569 4.703 1 80 ? PA UPG 335 A 1 HETATM 19 O O1A UPG . . . D 3 11.743 30.683 5.867 1 79.34 ? O1A UPG 335 A 1 HETATM 20 O O2A UPG . . . D 3 12.958 29.533 3.734 1 80 ? O2A UPG 335 A 1 HETATM 21 O O3A UPG . . . D 3 10.45 29.755 3.675 1 80 ? O3A UPG 335 A 1 HETATM 22 P PB UPG . . . D 3 9.004 30.41 3.895 1 80 ? PB UPG 335 A 1 HETATM 23 O O1B UPG . . . D 3 8.423 30.245 5.393 1 79.17 ? O1B UPG 335 A 1 HETATM 24 O O2B UPG . . . D 3 8.1 29.716 2.748 1 79.91 ? O2B UPG 335 A 1 HETATM 25 O O3B UPG . . . D 3 9.189 31.944 3.393 1 80 ? O3B UPG 335 A 1 HETATM 26 C C1' UPG . . . D 3 10.257 32.196 2.486 0 79.99 ? C1' UPG 335 A 1 HETATM 27 C C2' UPG . . . D 3 10.943 33.518 2.806 0 80 ? C2' UPG 335 A 1 HETATM 28 C C3' UPG . . . D 3 10.013 34.699 2.577 0 80 ? C3' UPG 335 A 1 HETATM 29 C C4' UPG . . . D 3 9.34 34.605 1.219 0 80 ? C4' UPG 335 A 1 HETATM 30 C C5' UPG . . . D 3 8.631 33.261 1.102 0 80 ? C5' UPG 335 A 1 HETATM 31 C C6' UPG . . . D 3 7.957 33.136 -0.244 0 80 ? C6' UPG 335 A 1 HETATM 32 O O2' UPG . . . D 3 11.324 33.507 4.176 0 80 ? O2' UPG 335 A 1 HETATM 33 O O3' UPG . . . D 3 10.79 35.887 2.611 0 80 ? O3' UPG 335 A 1 HETATM 34 O O4' UPG . . . D 3 8.368 35.64 1.139 0 80 ? O4' UPG 335 A 1 HETATM 35 O O5' UPG . . . D 3 9.592 32.204 1.21 0 80 ? O5' UPG 335 A 1 HETATM 36 O O6' UPG . . . D 3 6.642 33.657 -0.118 0 80 ? O6' UPG 335 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #