data_4AY6 # _model_server_result.job_id IUYIX8potOTEwJxQ2_PpGQ _model_server_result.datetime_utc '2024-10-19 00:44:02' _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 4ay6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1200}' # _entry.id 4AY6 # _exptl.entry_id 4AY6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 623.419 _entity.id 4 _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 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 4AY6 _cell.length_a 275.439 _cell.length_b 275.439 _cell.length_c 142.632 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AY6 _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,J 1 1 B,F,K,L 2 1 C,G,M,N 3 1 D,H,O,P 4 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 J N N ? 4 L N N ? 4 N N N ? 4 P N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 E N DNP 7 E DNP 1395 1_555 E C TYR 6 E TYR 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 E C DNP 7 E DNP 1395 1_555 E N SER 8 E SER 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 F N DNP 7 F DNP 1395 1_555 F C TYR 6 F TYR 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.369 ? covale ? covale4 F C DNP 7 F DNP 1395 1_555 F N SER 8 F SER 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale5 G C DNP 7 G DNP 1395 1_555 G N SER 8 G SER 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.294 ? covale ? covale6 G N DNP 7 G DNP 1395 1_555 G C TYR 6 G TYR 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale7 H C DNP 7 H DNP 1395 1_555 H N SER 8 H SER 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale8 H N DNP 7 H DNP 1395 1_555 H C TYR 6 H TYR 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? # _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' # _atom_sites.entry_id 4AY6 _atom_sites.fract_transf_matrix[1][1] 0.003631 _atom_sites.fract_transf_matrix[1][2] 0.002096 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004192 _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] 0.007011 _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 I 3 SO4 A 1 1100 1100 SO4 SO4 . J 4 12V A 1 1200 1200 12V 12V . K 3 SO4 B 1 1100 1100 SO4 SO4 . L 4 12V B 1 1200 1200 12V 12V . M 3 SO4 C 1 1100 1100 SO4 SO4 . N 4 12V C 1 1200 1200 12V 12V . O 3 SO4 D 1 1100 1100 SO4 SO4 . P 4 12V D 1 1200 1200 12V 12V . # 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 . . . J 4 137.509 -22.92 29.818 1 31.12 ? N1 12V 1200 A 1 HETATM 2 C C2 12V . . . J 4 138.249 -22.728 28.695 1 30.48 ? C2 12V 1200 A 1 HETATM 3 O O2 12V . . . J 4 139.152 -23.48 28.341 1 29.93 ? O2 12V 1200 A 1 HETATM 4 N N3 12V . . . J 4 138.017 -21.627 27.894 1 31.26 ? N3 12V 1200 A 1 HETATM 5 C C4 12V . . . J 4 137.005 -20.719 28.23 1 31.24 ? C4 12V 1200 A 1 HETATM 6 O O4 12V . . . J 4 136.817 -19.765 27.489 1 32.51 ? O4 12V 1200 A 1 HETATM 7 C C5 12V . . . J 4 136.227 -20.888 29.365 1 29.83 ? C5 12V 1200 A 1 HETATM 8 C C6 12V . . . J 4 136.474 -21.999 30.158 1 31.01 ? C6 12V 1200 A 1 HETATM 9 P PA 12V . . . J 4 133.492 -26.435 34.126 1 34.69 ? PA 12V 1200 A 1 HETATM 10 P PB 12V . . . J 4 134.117 -25.67 36.845 1 43.7 ? PB 12V 1200 A 1 HETATM 11 C C1' 12V . . . J 4 134.065 -28.212 37.361 1 52.92 ? C1' 12V 1200 A 1 HETATM 12 O O1' 12V . . . J 4 134.628 -26.902 37.68 1 46.15 ? O1' 12V 1200 A 1 HETATM 13 O O1A 12V . . . J 4 132.971 -27.795 34.315 1 34.65 ? O1A 12V 1200 A 1 HETATM 14 C C1B 12V . . . J 4 137.739 -24.139 30.667 1 31.07 ? C1B 12V 1200 A 1 HETATM 15 O O1B 12V . . . J 4 134.856 -24.456 37.257 1 43.27 ? O1B 12V 1200 A 1 HETATM 16 C C2' 12V . . . J 4 133.36 -28.889 38.547 1 56.9 ? C2' 12V 1200 A 1 HETATM 17 N N2' 12V . . . J 4 132.281 -27.986 38.971 1 59.33 ? N2' 12V 1200 A 1 HETATM 18 O O2' 12V . . . J 4 139.408 -23.671 32.293 1 34.35 ? O2' 12V 1200 A 1 HETATM 19 O O2A 12V . . . J 4 132.515 -25.308 34.05 1 36.51 ? O2A 12V 1200 A 1 HETATM 20 C C2B 12V . . . J 4 138.036 -23.971 32.133 1 30.89 ? C2B 12V 1200 A 1 HETATM 21 O O2B 12V . . . J 4 132.621 -25.7 36.92 1 45.06 ? O2B 12V 1200 A 1 HETATM 22 C C3' 12V . . . J 4 134.36 -29.189 39.679 1 58.69 ? C3' 12V 1200 A 1 HETATM 23 O O3' 12V . . . J 4 133.659 -29.571 40.885 1 58.43 ? O3' 12V 1200 A 1 HETATM 24 O O3A 12V . . . J 4 134.583 -26.115 35.355 1 39.11 ? O3A 12V 1200 A 1 HETATM 25 C C3B 12V . . . J 4 137.783 -25.386 32.591 1 29.39 ? C3B 12V 1200 A 1 HETATM 26 O O3B 12V . . . J 4 138.786 -26.289 32.034 1 28.33 ? O3B 12V 1200 A 1 HETATM 27 C C4' 12V . . . J 4 135.393 -30.279 39.295 1 58.55 ? C4' 12V 1200 A 1 HETATM 28 O O4' 12V . . . J 4 136.327 -30.404 40.381 1 59.01 ? O4' 12V 1200 A 1 HETATM 29 C C4B 12V . . . J 4 136.49 -25.656 31.9 1 29.9 ? C4B 12V 1200 A 1 HETATM 30 O O4B 12V . . . J 4 136.458 -24.755 30.761 1 30.82 ? O4B 12V 1200 A 1 HETATM 31 C C5' 12V . . . J 4 136.203 -29.906 38.06 1 57.37 ? C5' 12V 1200 A 1 HETATM 32 S S5' 12V . . . J 4 135.351 -29.234 36.673 1 55.45 ? S5' 12V 1200 A 1 HETATM 33 C C5B 12V . . . J 4 135.32 -25.301 32.783 1 29.7 ? C5B 12V 1200 A 1 HETATM 34 O O5B 12V . . . J 4 134.458 -26.421 32.882 1 30.52 ? O5B 12V 1200 A 1 HETATM 35 C C6' 12V . . . J 4 136.621 -31.144 37.274 1 60.62 ? C6' 12V 1200 A 1 HETATM 36 O O6' 12V . . . J 4 136.877 -32.248 38.138 1 64.92 ? O6' 12V 1200 A 1 HETATM 37 C C7' 12V . . . J 4 131.025 -28.189 38.572 1 63.92 ? C7' 12V 1200 A 1 HETATM 38 O O7' 12V . . . J 4 130.671 -29.149 37.891 1 70.59 ? O7' 12V 1200 A 1 HETATM 39 C C8' 12V . . . J 4 130.011 -27.163 39.059 1 62.93 ? C8' 12V 1200 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #