data_4GZ5 # _model_server_result.job_id rxNcT8fESurflKSQmcmZcQ _model_server_result.datetime_utc '2024-11-23 19:19:45' _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 4gz5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1501}' # _entry.id 4GZ5 # _exptl.entry_id 4GZ5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 607.354 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _entity.pdbx_number_of_molecules 4 _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 4GZ5 _cell.length_a 272.039 _cell.length_b 272.039 _cell.length_c 142.08 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GZ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 PISA dodecameric 12 author_and_software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,H,I,Y 1 1 B,J,K,L,M,N,Z 2 1 C,O,P,Q,R,S 3 1 D,T,U,V,W,X,AA 4 1 D,T,U,V,W,X,AA 5 2,3,4 A,B,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,Y,Z 5 1,5,6 # 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' 1_554 x,y,z-1 1 0 0 0 1 0 0 0 1 0 0 -142.08 3 'crystal symmetry operation' 2_564 -y,x-y+1,z-1 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -136.0195 235.592685 -142.08 4 'crystal symmetry operation' 3_454 -x+y-1,-x,z-1 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -272.039 0 -142.08 5 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -136.0195 235.592685 0 6 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -272.039 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 J N N ? 2 O N N ? 2 T 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 362 n n C1' O1' UD1 sing 363 n n C1' O5' UD1 sing 364 n n C1' H1' UD1 sing 365 n n C2' C3' UD1 sing 366 n n C2' N2' UD1 sing 367 n n C2' H2' UD1 sing 368 n n C3' C4' UD1 sing 369 n n C3' O3' UD1 sing 370 n n C3' H3' UD1 sing 371 n n C4' C5' UD1 sing 372 n n C4' O4' UD1 sing 373 n n C4' H4' UD1 sing 374 n n C5' C6' UD1 sing 375 n n C5' O5' UD1 sing 376 n n C5' H5' UD1 sing 377 n n C6' O6' UD1 sing 378 n n C6' "H6'1" UD1 sing 379 n n C6' "H6'2" UD1 sing 380 n n C7' C8' UD1 sing 381 n n C7' N2' UD1 sing 382 n n C7' O7' UD1 doub 383 n n C8' "H8'1" UD1 sing 384 n n C8' "H8'2" UD1 sing 385 n n C8' "H8'3" UD1 sing 386 n n N2' HN2' UD1 sing 387 n n O1' PB UD1 sing 388 n n O3' HO3' UD1 sing 389 n n O4' HO4' UD1 sing 390 n n O6' HO6' UD1 sing 391 n n N1 C2 UD1 sing 392 n n N1 C6 UD1 sing 393 n n N1 C1B UD1 sing 394 n n C2 N3 UD1 sing 395 n n C2 O2 UD1 doub 396 n n N3 C4 UD1 sing 397 n n N3 HN3 UD1 sing 398 n n C4 C5 UD1 sing 399 n n C4 O4 UD1 doub 400 n n C5 C6 UD1 doub 401 n n C5 H5 UD1 sing 402 n n C6 H6 UD1 sing 403 n n C1B C2B UD1 sing 404 n n C1B O4B UD1 sing 405 n n C1B H1B UD1 sing 406 n n C2B O2' UD1 sing 407 n n C2B C3B UD1 sing 408 n n C2B H2B UD1 sing 409 n n O2' HO2' UD1 sing 410 n n C3B C4B UD1 sing 411 n n C3B O3B UD1 sing 412 n n C3B H3B UD1 sing 413 n n C4B O4B UD1 sing 414 n n C4B C5B UD1 sing 415 n n C4B H4B UD1 sing 416 n n O3B HO3A UD1 sing 417 n n C5B O5B UD1 sing 418 n n C5B "H5'1" UD1 sing 419 n n C5B "H5'2" UD1 sing 420 n n O5B PA UD1 sing 421 n n PA O1A UD1 doub 422 n n PA O2A UD1 sing 423 n n PA O3A UD1 sing 424 n n O2A HOA2 UD1 sing 425 n n O3A PB UD1 sing 426 n n PB O1B UD1 doub 427 n n PB O2B UD1 sing 428 n n O2B HOB2 UD1 sing 429 n n # _atom_sites.entry_id 4GZ5 _atom_sites.fract_transf_matrix[1][1] 0.003676 _atom_sites.fract_transf_matrix[1][2] 0.002122 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004245 _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] 0.007038 _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 E 2 UD1 A 1 1501 1501 UD1 UD1 . F 3 SO4 A 1 1502 1601 SO4 SO4 . G 3 SO4 A 1 1503 1602 SO4 SO4 . H 3 SO4 A 1 1504 1603 SO4 SO4 . I 3 SO4 A 1 1505 1604 SO4 SO4 . J 2 UD1 B 1 1501 1501 UD1 UD1 . K 3 SO4 B 1 1502 1601 SO4 SO4 . L 3 SO4 B 1 1503 1602 SO4 SO4 . M 3 SO4 B 1 1504 1603 SO4 SO4 . N 3 SO4 B 1 1505 1604 SO4 SO4 . O 2 UD1 C 1 1501 1501 UD1 UD1 . P 3 SO4 C 1 1502 1601 SO4 SO4 . Q 3 SO4 C 1 1503 1602 SO4 SO4 . R 3 SO4 C 1 1504 1603 SO4 SO4 . S 3 SO4 C 1 1505 1604 SO4 SO4 . T 2 UD1 D 1 1501 1501 UD1 UD1 . U 3 SO4 D 1 1502 1601 SO4 SO4 . V 3 SO4 D 1 1503 1602 SO4 SO4 . W 3 SO4 D 1 1504 1603 SO4 SO4 . X 3 SO4 D 1 1505 1604 SO4 SO4 . Y 4 HOH A 1 1601 4 HOH HOH . Y 4 HOH A 2 1602 8 HOH HOH . Y 4 HOH A 3 1603 9 HOH HOH . Z 4 HOH B 1 1601 3 HOH HOH . Z 4 HOH B 2 1602 10 HOH HOH . Z 4 HOH B 3 1603 12 HOH HOH . Z 4 HOH B 4 1604 16 HOH HOH . Z 4 HOH B 5 1605 17 HOH HOH . Z 4 HOH B 6 1606 18 HOH HOH . AA 4 HOH D 1 1601 1 HOH HOH . AA 4 HOH D 2 1602 2 HOH HOH . AA 4 HOH D 3 1603 7 HOH HOH . AA 4 HOH D 4 1604 11 HOH HOH . AA 4 HOH D 5 1605 13 HOH HOH . AA 4 HOH D 6 1606 14 HOH HOH . AA 4 HOH D 7 1607 15 HOH HOH . AA 4 HOH D 8 1608 19 HOH HOH . AA 4 HOH D 9 1609 20 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 . . . E 2 -131.915 28.757 36.994 1 96.5 ? C1' UD1 1501 A 1 HETATM 2 C C2' UD1 . . . E 2 -131.202 29.353 38.259 1 75.93 ? C2' UD1 1501 A 1 HETATM 3 C C3' UD1 . . . E 2 -132.215 29.493 39.414 1 75.65 ? C3' UD1 1501 A 1 HETATM 4 C C4' UD1 . . . E 2 -133.438 30.348 38.96 1 78.66 ? C4' UD1 1501 A 1 HETATM 5 C C5' UD1 . . . E 2 -133.997 29.808 37.603 1 97.1 ? C5' UD1 1501 A 1 HETATM 6 C C6' UD1 . . . E 2 -135.045 30.753 36.99 1 97.44 ? C6' UD1 1501 A 1 HETATM 7 C C7' UD1 . . . E 2 -128.796 28.761 38.396 1 75.82 ? C7' UD1 1501 A 1 HETATM 8 C C8' UD1 . . . E 2 -127.822 27.699 38.85 1 75.55 ? C8' UD1 1501 A 1 HETATM 9 N N2' UD1 . . . E 2 -130.109 28.465 38.624 1 75.98 ? N2' UD1 1501 A 1 HETATM 10 O O1' UD1 . . . E 2 -132.43 27.518 37.252 1 96.7 ? O1' UD1 1501 A 1 HETATM 11 O O3' UD1 . . . E 2 -131.596 30.141 40.486 1 74.84 ? O3' UD1 1501 A 1 HETATM 12 O O4' UD1 . . . E 2 -134.396 30.235 39.981 1 78.27 ? O4' UD1 1501 A 1 HETATM 13 O O5' UD1 . . . E 2 -132.964 29.652 36.649 1 96.64 ? O5' UD1 1501 A 1 HETATM 14 O O6' UD1 . . . E 2 -134.427 31.939 36.585 1 97.59 ? O6' UD1 1501 A 1 HETATM 15 O O7' UD1 . . . E 2 -128.417 29.804 37.865 1 75.83 ? O7' UD1 1501 A 1 HETATM 16 N N1 UD1 . . . E 2 -135.154 22.89 29.579 1 54.04 ? N1 UD1 1501 A 1 HETATM 17 C C2 UD1 . . . E 2 -136 22.529 28.455 1 55.41 ? C2 UD1 1501 A 1 HETATM 18 N N3 UD1 . . . E 2 -135.662 21.38 27.711 1 55.86 ? N3 UD1 1501 A 1 HETATM 19 C C4 UD1 . . . E 2 -134.684 20.616 28.166 1 56.14 ? C4 UD1 1501 A 1 HETATM 20 C C5 UD1 . . . E 2 -133.827 20.929 29.27 1 55.7 ? C5 UD1 1501 A 1 HETATM 21 C C6 UD1 . . . E 2 -134.183 22.026 30.008 1 54.96 ? C6 UD1 1501 A 1 HETATM 22 O O2 UD1 . . . E 2 -136.969 23.191 28.157 1 56.12 ? O2 UD1 1501 A 1 HETATM 23 O O4 UD1 . . . E 2 -134.335 19.562 27.409 1 56.68 ? O4 UD1 1501 A 1 HETATM 24 C C1B UD1 . . . E 2 -135.484 24.099 30.38 1 51.47 ? C1B UD1 1501 A 1 HETATM 25 C C2B UD1 . . . E 2 -136.297 23.809 31.652 1 54.25 ? C2B UD1 1501 A 1 HETATM 26 O O2' UD1 . . . E 2 -137.603 23.533 31.262 1 55.13 ? O2' UD1 1501 A 1 HETATM 27 C C3B UD1 . . . E 2 -136.062 25.145 32.385 1 56.39 ? C3B UD1 1501 A 1 HETATM 28 C C4B UD1 . . . E 2 -134.653 25.58 31.89 1 42.19 ? C4B UD1 1501 A 1 HETATM 29 O O4B UD1 . . . E 2 -134.33 24.707 30.807 1 46.29 ? O4B UD1 1501 A 1 HETATM 30 O O3B UD1 . . . E 2 -137.074 25.997 31.952 1 58.13 ? O3B UD1 1501 A 1 HETATM 31 C C5B UD1 . . . E 2 -133.518 25.398 32.903 1 38.9 ? C5B UD1 1501 A 1 HETATM 32 O O5B UD1 . . . E 2 -132.539 26.265 32.544 1 37.08 ? O5B UD1 1501 A 1 HETATM 33 P PA UD1 . . . E 2 -131.31 26.585 33.73 1 56.62 ? PA UD1 1501 A 1 HETATM 34 O O1A UD1 . . . E 2 -131.002 28.014 33.464 1 57.63 ? O1A UD1 1501 A 1 HETATM 35 O O2A UD1 . . . E 2 -130.403 25.425 33.462 1 56.95 ? O2A UD1 1501 A 1 HETATM 36 O O3A UD1 . . . E 2 -132.038 26.309 35.101 1 46.4 ? O3A UD1 1501 A 1 HETATM 37 P PB UD1 . . . E 2 -131.844 25.974 36.624 1 60.46 ? PB UD1 1501 A 1 HETATM 38 O O1B UD1 . . . E 2 -130.41 25.932 37.033 1 59.8 ? O1B UD1 1501 A 1 HETATM 39 O O2B UD1 . . . E 2 -132.835 25.001 37.175 1 59.25 ? O2B UD1 1501 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 39 #