data_2GNA # _model_server_result.job_id Ln5hnOMs9gUSD2_B0hjqLA _model_server_result.datetime_utc '2024-12-21 14:18:50' _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 2gna # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":335}' # _entry.id 2GNA # _exptl.entry_id 2GNA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _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 2GNA _cell.length_a 112.218 _cell.length_b 112.218 _cell.length_c 107.348 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GNA _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 56.109 97.183639 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 -56.109 97.183639 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id GDU _chem_comp.mon_nstd_flag . _chem_comp.name "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-D-GALACTOPYRANOSE # 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 GDU sing 83 n n N1 C6 GDU sing 84 n n N1 C1D GDU sing 85 n n C2 N3 GDU sing 86 n n C2 O2 GDU doub 87 n n N3 C4 GDU sing 88 n n N3 HN3 GDU sing 89 n n C4 C5 GDU sing 90 n n C4 O4 GDU doub 91 n n C5 C6 GDU doub 92 n n C5 H5 GDU sing 93 n n C6 H6 GDU sing 94 n n C1D C2D GDU sing 95 n n C1D O4D GDU sing 96 n n C1D H1D GDU sing 97 n n C2D O2D GDU sing 98 n n C2D C3D GDU sing 99 n n C2D H2D GDU sing 100 n n O2D HO2' GDU sing 101 n n C3D C4D GDU sing 102 n n C3D O3D GDU sing 103 n n C3D H3D GDU sing 104 n n C4D O4D GDU sing 105 n n C4D C5D GDU sing 106 n n C4D H4D GDU sing 107 n n O3D HO3' GDU sing 108 n n C5D O5D GDU sing 109 n n C5D "H5'1" GDU sing 110 n n C5D "H5'2" GDU sing 111 n n O5D PA GDU sing 112 n n PA O1A GDU doub 113 n n PA O2A GDU sing 114 n n PA O3A GDU sing 115 n n O2A HOA2 GDU sing 116 n n O3A PB GDU sing 117 n n PB O1B GDU doub 118 n n PB O2B GDU sing 119 n n PB O3B GDU sing 120 n n O2B HOB2 GDU sing 121 n n O3B C1' GDU sing 122 n n C1' C2' GDU sing 123 n n C1' O5' GDU sing 124 n n C1' H1' GDU sing 125 n n C2' C3' GDU sing 126 n n C2' O2' GDU sing 127 n n C2' H2' GDU sing 128 n n C3' C4' GDU sing 129 n n C3' O3' GDU sing 130 n n C3' H3' GDU sing 131 n n C4' C5' GDU sing 132 n n C4' O4' GDU sing 133 n n C4' H4' GDU sing 134 n n C5' C6' GDU sing 135 n n C5' O5' GDU sing 136 n n C5' H5' GDU sing 137 n n C6' O6' GDU sing 138 n n C6' "H6'1" GDU sing 139 n n C6' "H6'2" GDU sing 140 n n O2' HO2A GDU sing 141 n n O3' HO3A GDU sing 142 n n O4' HO4' GDU sing 143 n n O6' HO6' GDU sing 144 n n # _atom_sites.entry_id 2GNA _atom_sites.fract_transf_matrix[1][1] 0.008911 _atom_sites.fract_transf_matrix[1][2] 0.005145 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01029 _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 GDU A 1 335 335 GDU GDU . D 3 NAP A 1 334 334 NAP NAP . E 2 GDU B 1 335 335 GDU GDU . F 3 NAP B 1 334 334 NAP NAP . G 4 MES B 1 336 336 MES MES . H 5 HOH A 1 336 1 HOH HOH . H 5 HOH A 2 337 4 HOH HOH . H 5 HOH A 3 338 5 HOH HOH . H 5 HOH A 4 339 12 HOH HOH . H 5 HOH A 5 340 14 HOH HOH . H 5 HOH A 6 341 16 HOH HOH . H 5 HOH A 7 342 17 HOH HOH . H 5 HOH A 8 343 18 HOH HOH . H 5 HOH A 9 344 20 HOH HOH . H 5 HOH A 10 345 22 HOH HOH . H 5 HOH A 11 346 23 HOH HOH . H 5 HOH A 12 347 24 HOH HOH . H 5 HOH A 13 348 26 HOH HOH . H 5 HOH A 14 349 28 HOH HOH . H 5 HOH A 15 350 29 HOH HOH . H 5 HOH A 16 351 33 HOH HOH . H 5 HOH A 17 352 36 HOH HOH . H 5 HOH A 18 353 37 HOH HOH . H 5 HOH A 19 354 41 HOH HOH . H 5 HOH A 20 355 42 HOH HOH . H 5 HOH A 21 356 43 HOH HOH . H 5 HOH A 22 357 45 HOH HOH . H 5 HOH A 23 358 47 HOH HOH . H 5 HOH A 24 359 48 HOH HOH . H 5 HOH A 25 360 51 HOH HOH . H 5 HOH A 26 361 52 HOH HOH . H 5 HOH A 27 362 53 HOH HOH . H 5 HOH A 28 363 56 HOH HOH . H 5 HOH A 29 364 59 HOH HOH . H 5 HOH A 30 365 64 HOH HOH . H 5 HOH A 31 366 65 HOH HOH . H 5 HOH A 32 367 68 HOH HOH . H 5 HOH A 33 368 71 HOH HOH . H 5 HOH A 34 369 73 HOH HOH . H 5 HOH A 35 370 76 HOH HOH . H 5 HOH A 36 371 77 HOH HOH . H 5 HOH A 37 372 82 HOH HOH . H 5 HOH A 38 373 83 HOH HOH . H 5 HOH A 39 374 84 HOH HOH . H 5 HOH A 40 375 87 HOH HOH . H 5 HOH A 41 376 88 HOH HOH . H 5 HOH A 42 377 90 HOH HOH . H 5 HOH A 43 378 95 HOH HOH . H 5 HOH A 44 379 96 HOH HOH . H 5 HOH A 45 380 97 HOH HOH . H 5 HOH A 46 381 99 HOH HOH . H 5 HOH A 47 382 102 HOH HOH . H 5 HOH A 48 383 103 HOH HOH . H 5 HOH A 49 384 107 HOH HOH . H 5 HOH A 50 385 108 HOH HOH . H 5 HOH A 51 386 109 HOH HOH . H 5 HOH A 52 387 111 HOH HOH . H 5 HOH A 53 388 112 HOH HOH . H 5 HOH A 54 389 114 HOH HOH . H 5 HOH A 55 390 118 HOH HOH . H 5 HOH A 56 391 125 HOH HOH . H 5 HOH A 57 392 127 HOH HOH . H 5 HOH A 58 393 128 HOH HOH . H 5 HOH A 59 394 131 HOH HOH . H 5 HOH A 60 395 132 HOH HOH . H 5 HOH A 61 396 133 HOH HOH . H 5 HOH A 62 397 134 HOH HOH . H 5 HOH A 63 398 135 HOH HOH . H 5 HOH A 64 399 136 HOH HOH . H 5 HOH A 65 400 141 HOH HOH . H 5 HOH A 66 401 143 HOH HOH . H 5 HOH A 67 402 145 HOH HOH . H 5 HOH A 68 403 148 HOH HOH . H 5 HOH A 69 404 149 HOH HOH . H 5 HOH A 70 405 153 HOH HOH . H 5 HOH A 71 406 155 HOH HOH . H 5 HOH A 72 407 156 HOH HOH . H 5 HOH A 73 408 159 HOH HOH . H 5 HOH A 74 409 160 HOH HOH . H 5 HOH A 75 410 161 HOH HOH . H 5 HOH A 76 411 164 HOH HOH . H 5 HOH A 77 412 165 HOH HOH . H 5 HOH A 78 413 166 HOH HOH . H 5 HOH A 79 414 167 HOH HOH . H 5 HOH A 80 415 168 HOH HOH . H 5 HOH A 81 416 170 HOH HOH . H 5 HOH A 82 417 171 HOH HOH . I 5 HOH B 1 337 2 HOH HOH . I 5 HOH B 2 338 3 HOH HOH . I 5 HOH B 3 339 6 HOH HOH . I 5 HOH B 4 340 7 HOH HOH . I 5 HOH B 5 341 8 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 13 HOH HOH . I 5 HOH B 10 346 15 HOH HOH . I 5 HOH B 11 347 19 HOH HOH . I 5 HOH B 12 348 21 HOH HOH . I 5 HOH B 13 349 25 HOH HOH . I 5 HOH B 14 350 27 HOH HOH . I 5 HOH B 15 351 30 HOH HOH . I 5 HOH B 16 352 31 HOH HOH . I 5 HOH B 17 353 32 HOH HOH . I 5 HOH B 18 354 34 HOH HOH . I 5 HOH B 19 355 35 HOH HOH . I 5 HOH B 20 356 38 HOH HOH . I 5 HOH B 21 357 39 HOH HOH . I 5 HOH B 22 358 40 HOH HOH . I 5 HOH B 23 359 44 HOH HOH . I 5 HOH B 24 360 46 HOH HOH . I 5 HOH B 25 361 49 HOH HOH . I 5 HOH B 26 362 50 HOH HOH . I 5 HOH B 27 363 54 HOH HOH . I 5 HOH B 28 364 55 HOH HOH . I 5 HOH B 29 365 57 HOH HOH . I 5 HOH B 30 366 58 HOH HOH . I 5 HOH B 31 367 60 HOH HOH . I 5 HOH B 32 368 61 HOH HOH . I 5 HOH B 33 369 62 HOH HOH . I 5 HOH B 34 370 63 HOH HOH . I 5 HOH B 35 371 66 HOH HOH . I 5 HOH B 36 372 67 HOH HOH . I 5 HOH B 37 373 69 HOH HOH . I 5 HOH B 38 374 70 HOH HOH . I 5 HOH B 39 375 72 HOH HOH . I 5 HOH B 40 376 74 HOH HOH . I 5 HOH B 41 377 75 HOH HOH . I 5 HOH B 42 378 78 HOH HOH . I 5 HOH B 43 379 79 HOH HOH . I 5 HOH B 44 380 80 HOH HOH . I 5 HOH B 45 381 81 HOH HOH . I 5 HOH B 46 382 85 HOH HOH . I 5 HOH B 47 383 86 HOH HOH . I 5 HOH B 48 384 89 HOH HOH . I 5 HOH B 49 385 91 HOH HOH . I 5 HOH B 50 386 92 HOH HOH . I 5 HOH B 51 387 93 HOH HOH . I 5 HOH B 52 388 94 HOH HOH . I 5 HOH B 53 389 98 HOH HOH . I 5 HOH B 54 390 100 HOH HOH . I 5 HOH B 55 391 101 HOH HOH . I 5 HOH B 56 392 104 HOH HOH . I 5 HOH B 57 393 105 HOH HOH . I 5 HOH B 58 394 106 HOH HOH . I 5 HOH B 59 395 110 HOH HOH . I 5 HOH B 60 396 113 HOH HOH . I 5 HOH B 61 397 115 HOH HOH . I 5 HOH B 62 398 116 HOH HOH . I 5 HOH B 63 399 117 HOH HOH . I 5 HOH B 64 400 119 HOH HOH . I 5 HOH B 65 401 120 HOH HOH . I 5 HOH B 66 402 121 HOH HOH . I 5 HOH B 67 403 122 HOH HOH . I 5 HOH B 68 404 123 HOH HOH . I 5 HOH B 69 405 124 HOH HOH . I 5 HOH B 70 406 126 HOH HOH . I 5 HOH B 71 407 129 HOH HOH . I 5 HOH B 72 408 130 HOH HOH . I 5 HOH B 73 409 137 HOH HOH . I 5 HOH B 74 410 138 HOH HOH . I 5 HOH B 75 411 139 HOH HOH . I 5 HOH B 76 412 140 HOH HOH . I 5 HOH B 77 413 142 HOH HOH . I 5 HOH B 78 414 144 HOH HOH . I 5 HOH B 79 415 146 HOH HOH . I 5 HOH B 80 416 147 HOH HOH . I 5 HOH B 81 417 150 HOH HOH . I 5 HOH B 82 418 151 HOH HOH . I 5 HOH B 83 419 152 HOH HOH . I 5 HOH B 84 420 154 HOH HOH . I 5 HOH B 85 421 157 HOH HOH . I 5 HOH B 86 422 158 HOH HOH . I 5 HOH B 87 423 162 HOH HOH . I 5 HOH B 88 424 163 HOH HOH . I 5 HOH B 89 425 169 HOH HOH . I 5 HOH B 90 426 172 HOH HOH . I 5 HOH B 91 427 173 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 GDU . . . C 2 11.761 25.552 8.252 1 79.96 ? N1 GDU 335 A 1 HETATM 2 C C2 GDU . . . C 2 12.467 24.577 8.963 1 80 ? C2 GDU 335 A 1 HETATM 3 N N3 GDU . . . C 2 13.429 25.021 9.852 1 79.74 ? N3 GDU 335 A 1 HETATM 4 C C4 GDU . . . C 2 13.756 26.352 10.1 1 80 ? C4 GDU 335 A 1 HETATM 5 C C5 GDU . . . C 2 12.969 27.353 9.307 1 79.66 ? C5 GDU 335 A 1 HETATM 6 C C6 GDU . . . C 2 12.031 26.886 8.442 1 79.59 ? C6 GDU 335 A 1 HETATM 7 O O2 GDU . . . C 2 12.259 23.39 8.821 1 79.58 ? O2 GDU 335 A 1 HETATM 8 O O4 GDU . . . C 2 14.619 26.676 10.901 1 80 ? O4 GDU 335 A 1 HETATM 9 C C1D GDU . . . C 2 10.724 25.118 7.285 1 80 ? C1D GDU 335 A 1 HETATM 10 C C2D GDU . . . C 2 9.415 25.848 7.427 1 79.17 ? C2D GDU 335 A 1 HETATM 11 O O2D GDU . . . C 2 8.561 25.099 8.277 1 80 ? O2D GDU 335 A 1 HETATM 12 C C3D GDU . . . C 2 8.853 25.943 6.054 1 78.9 ? C3D GDU 335 A 1 HETATM 13 C C4D GDU . . . C 2 10.007 25.647 5.134 1 79.06 ? C4D GDU 335 A 1 HETATM 14 O O4D GDU . . . C 2 11.145 25.315 5.936 1 80 ? O4D GDU 335 A 1 HETATM 15 O O3D GDU . . . C 2 7.881 24.927 5.862 1 78.33 ? O3D GDU 335 A 1 HETATM 16 C C5D GDU . . . C 2 10.334 26.857 4.286 1 79.15 ? C5D GDU 335 A 1 HETATM 17 O O5D GDU . . . C 2 10.895 27.84 5.123 1 79.13 ? O5D GDU 335 A 1 HETATM 18 P PA GDU . . . C 2 10.203 29.301 5.098 1 79.96 ? PA GDU 335 A 1 HETATM 19 O O1A GDU . . . C 2 8.592 29.312 5.246 1 80 ? O1A GDU 335 A 1 HETATM 20 O O2A GDU . . . C 2 11 30.098 6.256 1 78.4 ? O2A GDU 335 A 1 HETATM 21 O O3A GDU . . . C 2 10.757 29.948 3.742 1 80 ? O3A GDU 335 A 1 HETATM 22 P PB GDU . . . C 2 12.278 30.008 3.23 1 80 ? PB GDU 335 A 1 HETATM 23 O O1B GDU . . . C 2 13.262 29.01 4.029 1 79.75 ? O1B GDU 335 A 1 HETATM 24 O O2B GDU . . . C 2 12.174 29.711 1.637 1 80 ? O2B GDU 335 A 1 HETATM 25 O O3B GDU . . . C 2 12.672 31.584 3.353 1 80 ? O3B GDU 335 A 1 HETATM 26 C C1' GDU . . . C 2 12.027 32.492 2.462 1 80 ? C1' GDU 335 A 1 HETATM 27 C C2' GDU . . . C 2 12.927 33.697 2.182 1 79.78 ? C2' GDU 335 A 1 HETATM 28 C C3' GDU . . . C 2 13.166 34.511 3.454 1 80 ? C3' GDU 335 A 1 HETATM 29 C C4' GDU . . . C 2 11.848 34.82 4.16 1 80 ? C4' GDU 335 A 1 HETATM 30 C C5' GDU . . . C 2 11.11 33.509 4.435 1 80 ? C5' GDU 335 A 1 HETATM 31 C C6' GDU . . . C 2 9.795 33.77 5.141 1 78.7 ? C6' GDU 335 A 1 HETATM 32 O O2' GDU . . . C 2 14.183 33.226 1.707 1 77.68 ? O2' GDU 335 A 1 HETATM 33 O O3' GDU . . . C 2 13.79 35.74 3.095 1 80 ? O3' GDU 335 A 1 HETATM 34 O O4' GDU . . . C 2 11.047 35.636 3.298 1 79.02 ? O4' GDU 335 A 1 HETATM 35 O O5' GDU . . . C 2 10.824 32.847 3.187 1 80 ? O5' GDU 335 A 1 HETATM 36 O O6' GDU . . . C 2 10.052 33.792 6.541 1 77.16 ? O6' GDU 335 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 36 #