data_3QDV # _model_server_result.job_id GgeZ9JeB-bGmIEwKVnQEBw _model_server_result.datetime_utc '2024-11-27 11:43:05' _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 3qdv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":145}' # _entry.id 3QDV # _exptl.entry_id 3QDV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-alpha-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 3QDV _cell.length_a 68.04 _cell.length_b 97.446 _cell.length_c 84.094 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QDV _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 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,B,C,D,E,F,G,H 1 1,2 A,C,D,G 2 1,2 B,E,F,H 3 1,2 # 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 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 covale ? covale1 A C ACE 1 A ACE 0 1_555 A N THR 2 A THR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 B C ACE 1 B ACE 0 1_555 B N THR 2 B THR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NDG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-glucopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-glucosamine;2-acetamido-2-deoxy-alpha-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE # 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 NDG sing 273 n n C1 O5 NDG sing 274 n n C1 O1 NDG sing 275 n n C1 H1 NDG sing 276 n n C2 C3 NDG sing 277 n n C2 N2 NDG sing 278 n n C2 H2 NDG sing 279 n n C3 C4 NDG sing 280 n n C3 O3 NDG sing 281 n n C3 H3 NDG sing 282 n n C4 C5 NDG sing 283 n n C4 O4 NDG sing 284 n n C4 H4 NDG sing 285 n n C5 C6 NDG sing 286 n n C5 O5 NDG sing 287 n n C5 H5 NDG sing 288 n n C6 O6 NDG sing 289 n n C6 H61 NDG sing 290 n n C6 H62 NDG sing 291 n n C7 C8 NDG sing 292 n n C7 O7 NDG doub 293 n n C7 N2 NDG sing 294 n n C8 H81 NDG sing 295 n n C8 H82 NDG sing 296 n n C8 H83 NDG sing 297 n n O3 HO3 NDG sing 298 n n O4 HO4 NDG sing 299 n n O6 HO6 NDG sing 300 n n N2 HN2 NDG sing 301 n n O1 HO1 NDG sing 302 n n # 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 NDG DGlcpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NDG N-acetyl-a-D-glucopyranosamine 'COMMON NAME' GMML 1 NDG a-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NDG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3QDV _atom_sites.fract_transf_matrix[1][1] 0.014697 _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] 0.010262 _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] 0.011891 _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 A2G A 1 144 144 A2G NGA . D 3 NDG A 1 145 145 NDG NAG . E 2 A2G B 1 144 144 A2G NGA . F 3 NDG B 1 145 145 NDG NAG . G 4 HOH A 1 143 143 HOH HOH . G 4 HOH A 2 146 146 HOH HOH . G 4 HOH A 3 147 1 HOH HOH . G 4 HOH A 4 148 148 HOH HOH . G 4 HOH A 5 149 149 HOH HOH . G 4 HOH A 6 150 2 HOH HOH . G 4 HOH A 7 151 151 HOH HOH . G 4 HOH A 8 152 152 HOH HOH . G 4 HOH A 9 153 3 HOH HOH . G 4 HOH A 10 154 154 HOH HOH . G 4 HOH A 11 155 4 HOH HOH . G 4 HOH A 12 156 6 HOH HOH . G 4 HOH A 13 157 157 HOH HOH . G 4 HOH A 14 158 158 HOH HOH . G 4 HOH A 15 159 159 HOH HOH . G 4 HOH A 16 160 160 HOH HOH . G 4 HOH A 17 161 161 HOH HOH . G 4 HOH A 18 162 162 HOH HOH . G 4 HOH A 19 163 163 HOH HOH . G 4 HOH A 20 164 164 HOH HOH . G 4 HOH A 21 165 165 HOH HOH . G 4 HOH A 22 166 166 HOH HOH . G 4 HOH A 23 167 10 HOH HOH . G 4 HOH A 24 168 14 HOH HOH . G 4 HOH A 25 169 169 HOH HOH . G 4 HOH A 26 170 170 HOH HOH . G 4 HOH A 27 171 16 HOH HOH . G 4 HOH A 28 172 17 HOH HOH . G 4 HOH A 29 173 18 HOH HOH . G 4 HOH A 30 174 20 HOH HOH . G 4 HOH A 31 175 21 HOH HOH . G 4 HOH A 32 176 176 HOH HOH . G 4 HOH A 33 177 23 HOH HOH . G 4 HOH A 34 178 24 HOH HOH . G 4 HOH A 35 179 26 HOH HOH . G 4 HOH A 36 180 27 HOH HOH . G 4 HOH A 37 181 29 HOH HOH . G 4 HOH A 38 182 33 HOH HOH . G 4 HOH A 39 183 183 HOH HOH . G 4 HOH A 40 184 34 HOH HOH . G 4 HOH A 41 185 185 HOH HOH . G 4 HOH A 42 186 37 HOH HOH . G 4 HOH A 43 187 187 HOH HOH . G 4 HOH A 44 188 38 HOH HOH . G 4 HOH A 45 189 189 HOH HOH . G 4 HOH A 46 190 190 HOH HOH . G 4 HOH A 47 191 191 HOH HOH . G 4 HOH A 48 192 192 HOH HOH . G 4 HOH A 49 193 193 HOH HOH . G 4 HOH A 50 194 194 HOH HOH . G 4 HOH A 51 195 195 HOH HOH . G 4 HOH A 52 196 40 HOH HOH . G 4 HOH A 53 197 42 HOH HOH . G 4 HOH A 54 198 47 HOH HOH . G 4 HOH A 55 199 199 HOH HOH . G 4 HOH A 56 200 200 HOH HOH . G 4 HOH A 57 201 201 HOH HOH . G 4 HOH A 58 202 49 HOH HOH . G 4 HOH A 59 203 54 HOH HOH . G 4 HOH A 60 204 55 HOH HOH . G 4 HOH A 61 205 56 HOH HOH . G 4 HOH A 62 206 58 HOH HOH . G 4 HOH A 63 207 59 HOH HOH . G 4 HOH A 64 208 60 HOH HOH . G 4 HOH A 65 209 70 HOH HOH . G 4 HOH A 66 210 71 HOH HOH . G 4 HOH A 67 211 72 HOH HOH . G 4 HOH A 68 212 74 HOH HOH . G 4 HOH A 69 213 75 HOH HOH . G 4 HOH A 70 214 85 HOH HOH . G 4 HOH A 71 215 87 HOH HOH . G 4 HOH A 72 216 90 HOH HOH . G 4 HOH A 73 217 91 HOH HOH . G 4 HOH A 74 218 95 HOH HOH . G 4 HOH A 75 219 96 HOH HOH . G 4 HOH A 76 220 97 HOH HOH . G 4 HOH A 77 221 99 HOH HOH . G 4 HOH A 78 222 101 HOH HOH . G 4 HOH A 79 223 109 HOH HOH . G 4 HOH A 80 224 115 HOH HOH . G 4 HOH A 81 225 116 HOH HOH . G 4 HOH A 82 226 118 HOH HOH . G 4 HOH A 83 227 121 HOH HOH . G 4 HOH A 84 228 124 HOH HOH . G 4 HOH A 85 229 126 HOH HOH . G 4 HOH A 86 230 128 HOH HOH . G 4 HOH A 87 231 129 HOH HOH . G 4 HOH A 88 232 130 HOH HOH . G 4 HOH A 89 233 131 HOH HOH . G 4 HOH A 90 234 132 HOH HOH . G 4 HOH A 91 235 134 HOH HOH . G 4 HOH A 92 236 135 HOH HOH . G 4 HOH A 93 237 136 HOH HOH . G 4 HOH A 94 238 138 HOH HOH . G 4 HOH A 95 239 141 HOH HOH . G 4 HOH A 96 240 144 HOH HOH . H 4 HOH B 1 143 5 HOH HOH . H 4 HOH B 2 146 7 HOH HOH . H 4 HOH B 3 147 147 HOH HOH . H 4 HOH B 4 148 8 HOH HOH . H 4 HOH B 5 149 9 HOH HOH . H 4 HOH B 6 150 150 HOH HOH . H 4 HOH B 7 151 11 HOH HOH . H 4 HOH B 8 152 12 HOH HOH . H 4 HOH B 9 153 153 HOH HOH . H 4 HOH B 10 154 13 HOH HOH . H 4 HOH B 11 155 155 HOH HOH . H 4 HOH B 12 156 156 HOH HOH . H 4 HOH B 13 157 15 HOH HOH . H 4 HOH B 14 158 19 HOH HOH . H 4 HOH B 15 159 22 HOH HOH . H 4 HOH B 16 160 25 HOH HOH . H 4 HOH B 17 161 28 HOH HOH . H 4 HOH B 18 162 30 HOH HOH . H 4 HOH B 19 163 31 HOH HOH . H 4 HOH B 20 164 32 HOH HOH . H 4 HOH B 21 165 35 HOH HOH . H 4 HOH B 22 166 36 HOH HOH . H 4 HOH B 23 167 167 HOH HOH . H 4 HOH B 24 168 168 HOH HOH . H 4 HOH B 25 169 39 HOH HOH . H 4 HOH B 26 170 41 HOH HOH . H 4 HOH B 27 171 171 HOH HOH . H 4 HOH B 28 172 172 HOH HOH . H 4 HOH B 29 173 173 HOH HOH . H 4 HOH B 30 174 174 HOH HOH . H 4 HOH B 31 175 175 HOH HOH . H 4 HOH B 32 176 43 HOH HOH . H 4 HOH B 33 177 177 HOH HOH . H 4 HOH B 34 178 178 HOH HOH . H 4 HOH B 35 179 179 HOH HOH . H 4 HOH B 36 180 180 HOH HOH . H 4 HOH B 37 181 181 HOH HOH . H 4 HOH B 38 182 182 HOH HOH . H 4 HOH B 39 183 44 HOH HOH . H 4 HOH B 40 184 184 HOH HOH . H 4 HOH B 41 185 45 HOH HOH . H 4 HOH B 42 186 186 HOH HOH . H 4 HOH B 43 187 46 HOH HOH . H 4 HOH B 44 188 188 HOH HOH . H 4 HOH B 45 189 48 HOH HOH . H 4 HOH B 46 190 50 HOH HOH . H 4 HOH B 47 191 51 HOH HOH . H 4 HOH B 48 192 52 HOH HOH . H 4 HOH B 49 193 53 HOH HOH . H 4 HOH B 50 194 57 HOH HOH . H 4 HOH B 51 195 61 HOH HOH . H 4 HOH B 52 196 196 HOH HOH . H 4 HOH B 53 197 197 HOH HOH . H 4 HOH B 54 198 198 HOH HOH . H 4 HOH B 55 199 62 HOH HOH . H 4 HOH B 56 200 63 HOH HOH . H 4 HOH B 57 201 64 HOH HOH . H 4 HOH B 58 202 202 HOH HOH . H 4 HOH B 59 203 65 HOH HOH . H 4 HOH B 60 204 66 HOH HOH . H 4 HOH B 61 205 67 HOH HOH . H 4 HOH B 62 206 68 HOH HOH . H 4 HOH B 63 207 69 HOH HOH . H 4 HOH B 64 208 73 HOH HOH . H 4 HOH B 65 209 76 HOH HOH . H 4 HOH B 66 210 77 HOH HOH . H 4 HOH B 67 211 78 HOH HOH . H 4 HOH B 68 212 79 HOH HOH . H 4 HOH B 69 213 80 HOH HOH . H 4 HOH B 70 214 81 HOH HOH . H 4 HOH B 71 215 82 HOH HOH . H 4 HOH B 72 216 83 HOH HOH . H 4 HOH B 73 217 84 HOH HOH . H 4 HOH B 74 218 86 HOH HOH . H 4 HOH B 75 219 88 HOH HOH . H 4 HOH B 76 220 89 HOH HOH . H 4 HOH B 77 221 92 HOH HOH . H 4 HOH B 78 222 93 HOH HOH . H 4 HOH B 79 223 94 HOH HOH . H 4 HOH B 80 224 98 HOH HOH . H 4 HOH B 81 225 100 HOH HOH . H 4 HOH B 82 226 102 HOH HOH . H 4 HOH B 83 227 103 HOH HOH . H 4 HOH B 84 228 104 HOH HOH . H 4 HOH B 85 229 105 HOH HOH . H 4 HOH B 86 230 106 HOH HOH . H 4 HOH B 87 231 107 HOH HOH . H 4 HOH B 88 232 108 HOH HOH . H 4 HOH B 89 233 110 HOH HOH . H 4 HOH B 90 234 111 HOH HOH . H 4 HOH B 91 235 112 HOH HOH . H 4 HOH B 92 236 113 HOH HOH . H 4 HOH B 93 237 114 HOH HOH . H 4 HOH B 94 238 117 HOH HOH . H 4 HOH B 95 239 119 HOH HOH . H 4 HOH B 96 240 120 HOH HOH . H 4 HOH B 97 241 122 HOH HOH . H 4 HOH B 98 242 123 HOH HOH . H 4 HOH B 99 243 125 HOH HOH . H 4 HOH B 100 244 127 HOH HOH . H 4 HOH B 101 245 133 HOH HOH . H 4 HOH B 102 246 137 HOH HOH . H 4 HOH B 103 247 139 HOH HOH . H 4 HOH B 104 248 140 HOH HOH . H 4 HOH B 105 249 142 HOH HOH . H 4 HOH B 106 250 145 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 NDG . . . D 3 -7.631 -17.95 3.188 1 8.49 ? C1 NDG 145 A 1 HETATM 2 C C2 NDG . . . D 3 -9.09 -18.385 3.062 1 8.23 ? C2 NDG 145 A 1 HETATM 3 C C3 NDG . . . D 3 -9.376 -18.952 1.668 1 6.29 ? C3 NDG 145 A 1 HETATM 4 C C4 NDG . . . D 3 -8.883 -17.982 0.598 1 6.43 ? C4 NDG 145 A 1 HETATM 5 C C5 NDG . . . D 3 -7.402 -17.695 0.84 1 6.77 ? C5 NDG 145 A 1 HETATM 6 C C6 NDG . . . D 3 -6.813 -16.75 -0.214 1 8.15 ? C6 NDG 145 A 1 HETATM 7 C C7 NDG . . . D 3 -10.475 -19.353 4.846 1 7.69 ? C7 NDG 145 A 1 HETATM 8 C C8 NDG . . . D 3 -10.634 -20.457 5.856 1 10.68 ? C8 NDG 145 A 1 HETATM 9 O O5 NDG . . . D 3 -7.263 -17.101 2.117 1 8.21 ? O5 NDG 145 A 1 HETATM 10 O O3 NDG . . . D 3 -10.757 -19.221 1.528 1 6.43 ? O3 NDG 145 A 1 HETATM 11 O O4 NDG . . . D 3 -9.068 -18.582 -0.668 1 6.54 ? O4 NDG 145 A 1 HETATM 12 O O6 NDG . . . D 3 -7.416 -15.46 -0.194 1 6.97 ? O6 NDG 145 A 1 HETATM 13 O O7 NDG . . . D 3 -11.333 -18.465 4.764 1 9.24 ? O7 NDG 145 A 1 HETATM 14 N N2 NDG . . . D 3 -9.383 -19.381 4.083 1 7.54 ? N2 NDG 145 A 1 HETATM 15 O O1 NDG . . . D 3 -6.796 -19.099 3.16 1 11.5 ? O1 NDG 145 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 38 _model_server_stats.element_count 15 #