data_4RYC # _model_server_result.job_id p1UDMjJhJQqxLdj6rA3xag _model_server_result.datetime_utc '2024-10-12 15:22:04' _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 4ryc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1000}' # _entry.id 4RYC # _exptl.entry_id 4RYC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 90 _cell.entry_id 4RYC _cell.length_a 141.719 _cell.length_b 141.719 _cell.length_c 141.719 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RYC _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # 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 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 1 A,B,C,D,E,F,G,H,I,J 3 1,2,3 # 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' 8_645 -z+1,x-1/2,-y+1/2 0 0 -1 1 0 0 0 -1 0 141.719 -70.8595 70.8595 3 'crystal symmetry operation' 11_556 y+1/2,-z+1/2,-x+1 0 1 0 0 0 -1 -1 0 0 70.8595 70.8595 141.719 # 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 F 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 disulf ? disulf1 A SG CYS 51 A CYS 45 1_555 A SG CYS 58 A CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 217 A CYS 206 1_555 A SG CYS 221 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 259 A CYS 249 1_555 A SG CYS 296 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 B SG CYS 51 B CYS 45 1_555 B SG CYS 58 B CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf5 B SG CYS 217 B CYS 206 1_555 B SG CYS 221 B CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 B SG CYS 259 B CYS 249 1_555 B SG CYS 296 B CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 75 A ASN 67 1_555 C C1 NAG . A NAG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 B ND2 ASN 75 B ASN 67 1_555 F C1 NAG . B NAG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4RYC _atom_sites.fract_transf_matrix[1][1] 0.007056 _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] 0.007056 _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] 0.007056 _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 NAG A 1 1000 1000 NAG NAG . D 3 3ZK A 1 1001 1001 3ZK LI1 . E 4 SO4 A 1 1002 1002 SO4 SO4 . F 2 NAG B 1 1000 1000 NAG NAG . G 3 3ZK B 1 1001 1001 3ZK LI1 . H 5 DMS B 1 1002 1002 DMS DMS . I 6 HOH A 1 1101 1 HOH HOH . I 6 HOH A 2 1102 2 HOH HOH . I 6 HOH A 3 1103 6 HOH HOH . I 6 HOH A 4 1104 7 HOH HOH . I 6 HOH A 5 1105 8 HOH HOH . I 6 HOH A 6 1106 9 HOH HOH . I 6 HOH A 7 1107 10 HOH HOH . I 6 HOH A 8 1108 13 HOH HOH . I 6 HOH A 9 1109 14 HOH HOH . I 6 HOH A 10 1110 16 HOH HOH . I 6 HOH A 11 1111 17 HOH HOH . I 6 HOH A 12 1112 18 HOH HOH . I 6 HOH A 13 1113 19 HOH HOH . I 6 HOH A 14 1114 21 HOH HOH . I 6 HOH A 15 1115 24 HOH HOH . I 6 HOH A 16 1116 27 HOH HOH . I 6 HOH A 17 1117 28 HOH HOH . I 6 HOH A 18 1118 29 HOH HOH . I 6 HOH A 19 1119 33 HOH HOH . I 6 HOH A 20 1120 37 HOH HOH . I 6 HOH A 21 1121 41 HOH HOH . I 6 HOH A 22 1122 42 HOH HOH . I 6 HOH A 23 1123 44 HOH HOH . I 6 HOH A 24 1124 45 HOH HOH . I 6 HOH A 25 1125 47 HOH HOH . I 6 HOH A 26 1126 51 HOH HOH . I 6 HOH A 27 1127 52 HOH HOH . I 6 HOH A 28 1128 54 HOH HOH . I 6 HOH A 29 1129 55 HOH HOH . I 6 HOH A 30 1130 56 HOH HOH . I 6 HOH A 31 1131 58 HOH HOH . I 6 HOH A 32 1132 63 HOH HOH . I 6 HOH A 33 1133 64 HOH HOH . I 6 HOH A 34 1134 67 HOH HOH . I 6 HOH A 35 1135 70 HOH HOH . I 6 HOH A 36 1136 71 HOH HOH . I 6 HOH A 37 1137 72 HOH HOH . I 6 HOH A 38 1138 77 HOH HOH . I 6 HOH A 39 1139 78 HOH HOH . I 6 HOH A 40 1140 83 HOH HOH . I 6 HOH A 41 1141 84 HOH HOH . I 6 HOH A 42 1142 87 HOH HOH . I 6 HOH A 43 1143 88 HOH HOH . I 6 HOH A 44 1144 91 HOH HOH . I 6 HOH A 45 1145 92 HOH HOH . I 6 HOH A 46 1146 93 HOH HOH . I 6 HOH A 47 1147 97 HOH HOH . I 6 HOH A 48 1148 98 HOH HOH . I 6 HOH A 49 1149 100 HOH HOH . I 6 HOH A 50 1150 101 HOH HOH . I 6 HOH A 51 1151 102 HOH HOH . I 6 HOH A 52 1152 103 HOH HOH . I 6 HOH A 53 1153 106 HOH HOH . I 6 HOH A 54 1154 107 HOH HOH . I 6 HOH A 55 1155 108 HOH HOH . I 6 HOH A 56 1156 110 HOH HOH . I 6 HOH A 57 1157 115 HOH HOH . I 6 HOH A 58 1158 117 HOH HOH . I 6 HOH A 59 1159 118 HOH HOH . I 6 HOH A 60 1160 119 HOH HOH . I 6 HOH A 61 1161 120 HOH HOH . I 6 HOH A 62 1162 121 HOH HOH . I 6 HOH A 63 1163 123 HOH HOH . I 6 HOH A 64 1164 124 HOH HOH . I 6 HOH A 65 1165 125 HOH HOH . I 6 HOH A 66 1166 130 HOH HOH . I 6 HOH A 67 1167 131 HOH HOH . I 6 HOH A 68 1168 132 HOH HOH . I 6 HOH A 69 1169 133 HOH HOH . I 6 HOH A 70 1170 136 HOH HOH . I 6 HOH A 71 1171 138 HOH HOH . I 6 HOH A 72 1172 139 HOH HOH . I 6 HOH A 73 1173 140 HOH HOH . I 6 HOH A 74 1174 141 HOH HOH . I 6 HOH A 75 1175 142 HOH HOH . I 6 HOH A 76 1176 143 HOH HOH . I 6 HOH A 77 1177 144 HOH HOH . I 6 HOH A 78 1178 145 HOH HOH . I 6 HOH A 79 1179 149 HOH HOH . I 6 HOH A 80 1180 150 HOH HOH . I 6 HOH A 81 1181 152 HOH HOH . I 6 HOH A 82 1182 153 HOH HOH . I 6 HOH A 83 1183 157 HOH HOH . I 6 HOH A 84 1184 159 HOH HOH . I 6 HOH A 85 1185 161 HOH HOH . I 6 HOH A 86 1186 163 HOH HOH . I 6 HOH A 87 1187 165 HOH HOH . I 6 HOH A 88 1188 166 HOH HOH . I 6 HOH A 89 1189 167 HOH HOH . I 6 HOH A 90 1190 168 HOH HOH . I 6 HOH A 91 1191 170 HOH HOH . I 6 HOH A 92 1192 171 HOH HOH . I 6 HOH A 93 1193 173 HOH HOH . I 6 HOH A 94 1194 174 HOH HOH . I 6 HOH A 95 1195 175 HOH HOH . I 6 HOH A 96 1196 183 HOH HOH . I 6 HOH A 97 1197 184 HOH HOH . I 6 HOH A 98 1198 185 HOH HOH . I 6 HOH A 99 1199 186 HOH HOH . I 6 HOH A 100 1200 188 HOH HOH . I 6 HOH A 101 1201 189 HOH HOH . I 6 HOH A 102 1202 190 HOH HOH . I 6 HOH A 103 1203 192 HOH HOH . I 6 HOH A 104 1204 198 HOH HOH . I 6 HOH A 105 1205 200 HOH HOH . I 6 HOH A 106 1206 201 HOH HOH . I 6 HOH A 107 1207 203 HOH HOH . I 6 HOH A 108 1208 204 HOH HOH . I 6 HOH A 109 1209 205 HOH HOH . I 6 HOH A 110 1210 206 HOH HOH . I 6 HOH A 111 1211 207 HOH HOH . I 6 HOH A 112 1212 208 HOH HOH . I 6 HOH A 113 1213 210 HOH HOH . I 6 HOH A 114 1214 213 HOH HOH . I 6 HOH A 115 1215 215 HOH HOH . I 6 HOH A 116 1216 216 HOH HOH . I 6 HOH A 117 1217 217 HOH HOH . I 6 HOH A 118 1218 218 HOH HOH . I 6 HOH A 119 1219 219 HOH HOH . I 6 HOH A 120 1220 221 HOH HOH . J 6 HOH B 1 1101 3 HOH HOH . J 6 HOH B 2 1102 4 HOH HOH . J 6 HOH B 3 1103 5 HOH HOH . J 6 HOH B 4 1104 11 HOH HOH . J 6 HOH B 5 1105 12 HOH HOH . J 6 HOH B 6 1106 15 HOH HOH . J 6 HOH B 7 1107 20 HOH HOH . J 6 HOH B 8 1108 22 HOH HOH . J 6 HOH B 9 1109 23 HOH HOH . J 6 HOH B 10 1110 25 HOH HOH . J 6 HOH B 11 1111 26 HOH HOH . J 6 HOH B 12 1112 30 HOH HOH . J 6 HOH B 13 1113 31 HOH HOH . J 6 HOH B 14 1114 32 HOH HOH . J 6 HOH B 15 1115 34 HOH HOH . J 6 HOH B 16 1116 35 HOH HOH . J 6 HOH B 17 1117 36 HOH HOH . J 6 HOH B 18 1118 38 HOH HOH . J 6 HOH B 19 1119 39 HOH HOH . J 6 HOH B 20 1120 40 HOH HOH . J 6 HOH B 21 1121 43 HOH HOH . J 6 HOH B 22 1122 46 HOH HOH . J 6 HOH B 23 1123 48 HOH HOH . J 6 HOH B 24 1124 49 HOH HOH . J 6 HOH B 25 1125 50 HOH HOH . J 6 HOH B 26 1126 53 HOH HOH . J 6 HOH B 27 1127 57 HOH HOH . J 6 HOH B 28 1128 59 HOH HOH . J 6 HOH B 29 1129 60 HOH HOH . J 6 HOH B 30 1130 61 HOH HOH . J 6 HOH B 31 1131 62 HOH HOH . J 6 HOH B 32 1132 65 HOH HOH . J 6 HOH B 33 1133 66 HOH HOH . J 6 HOH B 34 1134 68 HOH HOH . J 6 HOH B 35 1135 69 HOH HOH . J 6 HOH B 36 1136 73 HOH HOH . J 6 HOH B 37 1137 74 HOH HOH . J 6 HOH B 38 1138 75 HOH HOH . J 6 HOH B 39 1139 76 HOH HOH . J 6 HOH B 40 1140 79 HOH HOH . J 6 HOH B 41 1141 80 HOH HOH . J 6 HOH B 42 1142 81 HOH HOH . J 6 HOH B 43 1143 82 HOH HOH . J 6 HOH B 44 1144 85 HOH HOH . J 6 HOH B 45 1145 86 HOH HOH . J 6 HOH B 46 1146 89 HOH HOH . J 6 HOH B 47 1147 90 HOH HOH . J 6 HOH B 48 1148 94 HOH HOH . J 6 HOH B 49 1149 95 HOH HOH . J 6 HOH B 50 1150 96 HOH HOH . J 6 HOH B 51 1151 99 HOH HOH . J 6 HOH B 52 1152 104 HOH HOH . J 6 HOH B 53 1153 105 HOH HOH . J 6 HOH B 54 1154 109 HOH HOH . J 6 HOH B 55 1155 111 HOH HOH . J 6 HOH B 56 1156 112 HOH HOH . J 6 HOH B 57 1157 113 HOH HOH . J 6 HOH B 58 1158 114 HOH HOH . J 6 HOH B 59 1159 116 HOH HOH . J 6 HOH B 60 1160 122 HOH HOH . J 6 HOH B 61 1161 126 HOH HOH . J 6 HOH B 62 1162 127 HOH HOH . J 6 HOH B 63 1163 128 HOH HOH . J 6 HOH B 64 1164 129 HOH HOH . J 6 HOH B 65 1165 134 HOH HOH . J 6 HOH B 66 1166 135 HOH HOH . J 6 HOH B 67 1167 137 HOH HOH . J 6 HOH B 68 1168 146 HOH HOH . J 6 HOH B 69 1169 147 HOH HOH . J 6 HOH B 70 1170 148 HOH HOH . J 6 HOH B 71 1171 151 HOH HOH . J 6 HOH B 72 1172 154 HOH HOH . J 6 HOH B 73 1173 155 HOH HOH . J 6 HOH B 74 1174 156 HOH HOH . J 6 HOH B 75 1175 158 HOH HOH . J 6 HOH B 76 1176 160 HOH HOH . J 6 HOH B 77 1177 162 HOH HOH . J 6 HOH B 78 1178 164 HOH HOH . J 6 HOH B 79 1179 169 HOH HOH . J 6 HOH B 80 1180 172 HOH HOH . J 6 HOH B 81 1181 176 HOH HOH . J 6 HOH B 82 1182 177 HOH HOH . J 6 HOH B 83 1183 178 HOH HOH . J 6 HOH B 84 1184 179 HOH HOH . J 6 HOH B 85 1185 180 HOH HOH . J 6 HOH B 86 1186 181 HOH HOH . J 6 HOH B 87 1187 182 HOH HOH . J 6 HOH B 88 1188 187 HOH HOH . J 6 HOH B 89 1189 191 HOH HOH . J 6 HOH B 90 1190 193 HOH HOH . J 6 HOH B 91 1191 194 HOH HOH . J 6 HOH B 92 1192 195 HOH HOH . J 6 HOH B 93 1193 196 HOH HOH . J 6 HOH B 94 1194 197 HOH HOH . J 6 HOH B 95 1195 199 HOH HOH . J 6 HOH B 96 1196 202 HOH HOH . J 6 HOH B 97 1197 209 HOH HOH . J 6 HOH B 98 1198 211 HOH HOH . J 6 HOH B 99 1199 212 HOH HOH . J 6 HOH B 100 1200 214 HOH HOH . J 6 HOH B 101 1201 220 HOH HOH . J 6 HOH B 102 1202 222 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 NAG . . . F 2 78.863 21.039 -5.29 1 95.85 ? C1 NAG 1000 B 1 HETATM 2 C C2 NAG . . . F 2 78.483 20.625 -6.715 1 100.02 ? C2 NAG 1000 B 1 HETATM 3 C C3 NAG . . . F 2 78.416 21.889 -7.577 1 101.25 ? C3 NAG 1000 B 1 HETATM 4 C C4 NAG . . . F 2 77.476 22.924 -6.966 1 101.25 ? C4 NAG 1000 B 1 HETATM 5 C C5 NAG . . . F 2 77.896 23.241 -5.533 1 99.52 ? C5 NAG 1000 B 1 HETATM 6 C C6 NAG . . . F 2 76.938 24.166 -4.813 1 98 ? C6 NAG 1000 B 1 HETATM 7 C C7 NAG . . . F 2 79.27 18.366 -7.367 1 103.49 ? C7 NAG 1000 B 1 HETATM 8 C C8 NAG . . . F 2 80.361 17.605 -8.06 1 103.74 ? C8 NAG 1000 B 1 HETATM 9 N N2 NAG . . . F 2 79.457 19.694 -7.267 1 102.23 ? N2 NAG 1000 B 1 HETATM 10 O O3 NAG . . . F 2 78.003 21.563 -8.898 1 101.97 ? O3 NAG 1000 B 1 HETATM 11 O O4 NAG . . . F 2 77.524 24.122 -7.737 1 102.5 ? O4 NAG 1000 B 1 HETATM 12 O O5 NAG . . . F 2 77.963 22.025 -4.765 1 98.5 ? O5 NAG 1000 B 1 HETATM 13 O O6 NAG . . . F 2 77.478 24.65 -3.587 1 96.19 ? O6 NAG 1000 B 1 HETATM 14 O O7 NAG . . . F 2 78.272 17.807 -6.916 1 103.6 ? O7 NAG 1000 B 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #