data_5BNW # _model_server_result.job_id 741ANiRFfXHPtrCyztpmUg _model_server_result.datetime_utc '2024-11-29 11:52:07' _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 5bnw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1101}' # _entry.id 5BNW # _exptl.entry_id 5BNW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 623.419 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' _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 5BNW _cell.length_a 138.183 _cell.length_b 150.176 _cell.length_c 199.241 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BNW _symmetry.cell_setting ? _symmetry.Int_Tables_number 22 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'F 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C17 H27 N3 O16 P2 S' _chem_comp.formula_weight 623.419 _chem_comp.id 12V _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE' # 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 C1B N1 12V sing 1 n n C2 N1 12V sing 2 n n N1 C6 12V sing 3 n n O2 C2 12V doub 4 n n C2 N3 12V sing 5 n n N3 C4 12V sing 6 n n C4 O4 12V doub 7 n n C4 C5 12V sing 8 n n C6 C5 12V doub 9 n n C5 H5 12V sing 10 n n C6 H6 12V sing 11 n n O5B PA 12V sing 12 n n O1A PA 12V doub 13 n n PA O3A 12V sing 14 n n PA O2A 12V sing 15 n n O3A PB 12V sing 16 n n O1' PB 12V sing 17 n n PB O1B 12V doub 18 n n PB O2B 12V sing 19 n n S5' C1' 12V sing 20 n n C1' C2' 12V sing 21 n n C1' O1' 12V sing 22 n n C1' H1' 12V sing 23 n n C1B O4B 12V sing 24 n n C1B C2B 12V sing 25 n n C1B H1B 12V sing 26 n n C3' C2' 12V sing 27 n n C2' N2' 12V sing 28 n n C2' H2' 12V sing 29 n n N2' C7' 12V sing 30 n n N2' HN2' 12V sing 31 n n O2' C2B 12V sing 32 n n O2' HO2' 12V sing 33 n n O2A HO2A 12V sing 34 n n C3B C2B 12V sing 35 n n C2B H2B 12V sing 36 n n O2B HO2B 12V sing 37 n n C4' C3' 12V sing 38 n n C3' O3' 12V sing 39 n n C3' H3' 12V sing 40 n n O3' HO3' 12V sing 41 n n O3B C3B 12V sing 42 n n C3B C4B 12V sing 43 n n C3B H3B 12V sing 44 n n O3B HO3B 12V sing 45 n n C5' C4' 12V sing 46 n n O4' C4' 12V sing 47 n n C4' H4' 12V sing 48 n n O4' HO4' 12V sing 49 n n C4B O4B 12V sing 50 n n C4B C5B 12V sing 51 n n C4B H4B 12V sing 52 n n C6' C5' 12V sing 53 n n C5' S5' 12V sing 54 n n C5' H5' 12V sing 55 n n O5B C5B 12V sing 56 n n C5B H5B 12V sing 57 n n C5B H5BA 12V sing 58 n n O6' C6' 12V sing 59 n n C6' H6' 12V sing 60 n n C6' "H6'A" 12V sing 61 n n O6' HO6' 12V sing 62 n n O7' C7' 12V doub 63 n n C7' C8' 12V sing 64 n n C8' H8' 12V sing 65 n n C8' "H8'A" 12V sing 66 n n C8' "H8'B" 12V sing 67 n n N3 HN3 12V sing 68 n n # _atom_sites.entry_id 5BNW _atom_sites.fract_transf_matrix[1][1] 0.007237 _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] 0.006659 _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] 0.005019 _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 3 12V A 1 1101 1 12V UDS . D 4 HOH A 1 1201 89 HOH HOH . D 4 HOH A 2 1202 35 HOH HOH . D 4 HOH A 3 1203 95 HOH HOH . D 4 HOH A 4 1204 28 HOH HOH . D 4 HOH A 5 1205 88 HOH HOH . D 4 HOH A 6 1206 52 HOH HOH . D 4 HOH A 7 1207 38 HOH HOH . D 4 HOH A 8 1208 16 HOH HOH . D 4 HOH A 9 1209 12 HOH HOH . D 4 HOH A 10 1210 86 HOH HOH . D 4 HOH A 11 1211 58 HOH HOH . D 4 HOH A 12 1212 67 HOH HOH . D 4 HOH A 13 1213 97 HOH HOH . D 4 HOH A 14 1214 32 HOH HOH . D 4 HOH A 15 1215 3 HOH HOH . D 4 HOH A 16 1216 49 HOH HOH . D 4 HOH A 17 1217 94 HOH HOH . D 4 HOH A 18 1218 19 HOH HOH . D 4 HOH A 19 1219 43 HOH HOH . D 4 HOH A 20 1220 103 HOH HOH . D 4 HOH A 21 1221 99 HOH HOH . D 4 HOH A 22 1222 60 HOH HOH . D 4 HOH A 23 1223 54 HOH HOH . D 4 HOH A 24 1224 11 HOH HOH . D 4 HOH A 25 1225 27 HOH HOH . D 4 HOH A 26 1226 1 HOH HOH . D 4 HOH A 27 1227 64 HOH HOH . D 4 HOH A 28 1228 42 HOH HOH . D 4 HOH A 29 1229 56 HOH HOH . D 4 HOH A 30 1230 24 HOH HOH . D 4 HOH A 31 1231 69 HOH HOH . D 4 HOH A 32 1232 14 HOH HOH . D 4 HOH A 33 1233 10 HOH HOH . D 4 HOH A 34 1234 90 HOH HOH . D 4 HOH A 35 1235 50 HOH HOH . D 4 HOH A 36 1236 21 HOH HOH . D 4 HOH A 37 1237 66 HOH HOH . D 4 HOH A 38 1238 77 HOH HOH . D 4 HOH A 39 1239 59 HOH HOH . D 4 HOH A 40 1240 22 HOH HOH . D 4 HOH A 41 1241 93 HOH HOH . D 4 HOH A 42 1242 4 HOH HOH . D 4 HOH A 43 1243 31 HOH HOH . D 4 HOH A 44 1244 47 HOH HOH . D 4 HOH A 45 1245 51 HOH HOH . D 4 HOH A 46 1246 9 HOH HOH . D 4 HOH A 47 1247 18 HOH HOH . D 4 HOH A 48 1248 65 HOH HOH . D 4 HOH A 49 1249 101 HOH HOH . D 4 HOH A 50 1250 29 HOH HOH . D 4 HOH A 51 1251 57 HOH HOH . D 4 HOH A 52 1252 7 HOH HOH . D 4 HOH A 53 1253 6 HOH HOH . D 4 HOH A 54 1254 15 HOH HOH . D 4 HOH A 55 1255 92 HOH HOH . D 4 HOH A 56 1256 53 HOH HOH . D 4 HOH A 57 1257 20 HOH HOH . D 4 HOH A 58 1258 39 HOH HOH . D 4 HOH A 59 1259 98 HOH HOH . D 4 HOH A 60 1260 70 HOH HOH . D 4 HOH A 61 1261 8 HOH HOH . D 4 HOH A 62 1262 23 HOH HOH . D 4 HOH A 63 1263 30 HOH HOH . D 4 HOH A 64 1264 100 HOH HOH . D 4 HOH A 65 1265 25 HOH HOH . D 4 HOH A 66 1266 36 HOH HOH . D 4 HOH A 67 1267 44 HOH HOH . D 4 HOH A 68 1268 68 HOH HOH . D 4 HOH A 69 1269 5 HOH HOH . D 4 HOH A 70 1270 26 HOH HOH . D 4 HOH A 71 1271 34 HOH HOH . D 4 HOH A 72 1272 71 HOH HOH . D 4 HOH A 73 1273 2 HOH HOH . D 4 HOH A 74 1274 74 HOH HOH . D 4 HOH A 75 1275 17 HOH HOH . D 4 HOH A 76 1276 55 HOH HOH . D 4 HOH A 77 1277 87 HOH HOH . E 4 HOH D 1 201 83 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 12V . . . C 3 21.939 1.889 20.996 1 27.93 ? N1 12V 1101 A 1 HETATM 2 C C2 12V . . . C 3 21.506 0.658 20.644 1 27.59 ? C2 12V 1101 A 1 HETATM 3 O O2 12V . . . C 3 20.436 0.474 20.089 1 26.41 ? O2 12V 1101 A 1 HETATM 4 N N3 12V . . . C 3 22.229 -0.456 20.935 1 28.9 ? N3 12V 1101 A 1 HETATM 5 C C4 12V . . . C 3 23.434 -0.353 21.599 1 27.27 ? C4 12V 1101 A 1 HETATM 6 O O4 12V . . . C 3 24.038 -1.397 21.847 1 25.85 ? O4 12V 1101 A 1 HETATM 7 C C5 12V . . . C 3 23.897 0.9 21.954 1 26.94 ? C5 12V 1101 A 1 HETATM 8 C C6 12V . . . C 3 23.15 2.027 21.655 1 26.6 ? C6 12V 1101 A 1 HETATM 9 P PA 12V . . . C 3 23.6 8.387 19.478 1 29.92 ? PA 12V 1101 A 1 HETATM 10 P PB 12V . . . C 3 23.378 10.097 21.801 1 32.31 ? PB 12V 1101 A 1 HETATM 11 C C1' 12V . . . C 3 22.106 11.623 20.062 1 35.01 ? C1' 12V 1101 A 1 HETATM 12 O O1' 12V . . . C 3 22.184 11.077 21.409 1 34.07 ? O1' 12V 1101 A 1 HETATM 13 O O1A 12V . . . C 3 23.316 9.592 18.741 1 33.16 ? O1A 12V 1101 A 1 HETATM 14 C C1B 12V . . . C 3 21.11 3.073 20.599 1 26.75 ? C1B 12V 1101 A 1 HETATM 15 O O1B 12V . . . C 3 23.311 9.872 23.253 1 31.68 ? O1B 12V 1101 A 1 HETATM 16 C C2' 12V . . . C 3 22.307 13.142 20.053 1 37.03 ? C2' 12V 1101 A 1 HETATM 17 N N2' 12V . . . C 3 23.671 13.359 20.537 1 36.8 ? N2' 12V 1101 A 1 HETATM 18 O O2' 12V . . . C 3 19.689 3.899 22.395 1 24.99 ? O2' 12V 1101 A 1 HETATM 19 O O2A 12V . . . C 3 25.019 7.947 19.576 1 26.21 ? O2A 12V 1101 A 1 HETATM 20 C C2B 12V . . . C 3 20.894 4.157 21.584 1 26.22 ? C2B 12V 1101 A 1 HETATM 21 O O2B 12V . . . C 3 24.58 10.644 21.174 1 28.92 ? O2B 12V 1101 A 1 HETATM 22 C C3' 12V . . . C 3 21.296 13.854 20.954 1 38.17 ? C3' 12V 1101 A 1 HETATM 23 O O3' 12V . . . C 3 21.715 15.178 21.246 1 38.96 ? O3' 12V 1101 A 1 HETATM 24 O O3A 12V . . . C 3 23.011 8.685 21.027 1 31.02 ? O3A 12V 1101 A 1 HETATM 25 C C3B 12V . . . C 3 20.701 5.315 20.601 1 26.07 ? C3B 12V 1101 A 1 HETATM 26 O O3B 12V . . . C 3 19.355 5.311 20.075 1 26.41 ? O3B 12V 1101 A 1 HETATM 27 C C4' 12V . . . C 3 19.903 13.855 20.321 1 37.54 ? C4' 12V 1101 A 1 HETATM 28 O O4' 12V . . . C 3 19.096 14.528 21.293 1 34.95 ? O4' 12V 1101 A 1 HETATM 29 C C4B 12V . . . C 3 21.658 5.034 19.488 1 24.78 ? C4B 12V 1101 A 1 HETATM 30 O O4B 12V . . . C 3 22.039 3.649 19.681 1 25.51 ? O4B 12V 1101 A 1 HETATM 31 C C5' 12V . . . C 3 19.386 12.383 20.19 1 36.77 ? C5' 12V 1101 A 1 HETATM 32 S S5' 12V . . . C 3 20.522 11.277 19.367 1 37.14 ? S5' 12V 1101 A 1 HETATM 33 C C5B 12V . . . C 3 22.935 5.862 19.573 1 23.81 ? C5B 12V 1101 A 1 HETATM 34 O O5B 12V . . . C 3 22.689 7.161 19.043 1 27.23 ? O5B 12V 1101 A 1 HETATM 35 C C6' 12V . . . C 3 18.017 12.3 19.5 1 36.79 ? C6' 12V 1101 A 1 HETATM 36 O O6' 12V . . . C 3 18.105 12.693 18.111 1 33.7 ? O6' 12V 1101 A 1 HETATM 37 C C7' 12V . . . C 3 24.643 13.613 19.704 1 37.62 ? C7' 12V 1101 A 1 HETATM 38 O O7' 12V . . . C 3 24.465 13.758 18.515 1 48.72 ? O7' 12V 1101 A 1 HETATM 39 C C8' 12V . . . C 3 26.008 13.823 20.3 1 40.05 ? C8' 12V 1101 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #