data_1DFV # _model_server_result.job_id jzzGBwEL6NeVD57RKzMZKg _model_server_result.datetime_utc '2024-11-25 12:27:14' _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 1dfv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":178}' # _entry.id 1DFV # _exptl.entry_id 1DFV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 1DFV _cell.length_a 115.021 _cell.length_b 115.021 _cell.length_c 117.638 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DFV _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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 monomeric 1 author_and_software_defined_assembly 1 ? monomeric 1 author_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,C,D,E,H 1 1 B,F,G,I 2 1 B,F,G,I 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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 115.021 115.021 58.819 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG A 179 NAG 2 n C NAG 2 C 2 NAG A 180 NAG # 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 76 A CYS 76 1_555 A SG CYS 175 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 76 B CYS 76 1_555 B SG CYS 175 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 65 A ASN 65 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 B ND2 ASN 65 B ASN 65 1_555 F C1 NAG . B NAG 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.523 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? # _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_ _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 NAG sing 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 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 1DFV _atom_sites.fract_transf_matrix[1][1] 0.008694 _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] 0.008694 _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] 0.008501 _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 D 3 SO4 A 1 181 181 SO4 SO4 . E 3 SO4 A 1 183 183 SO4 SO4 . F 4 NAG B 1 178 178 NAG NAG . G 3 SO4 B 1 182 182 SO4 SO4 . H 5 HOH A 1 184 1 HOH HOH . H 5 HOH A 2 185 12 HOH HOH . H 5 HOH A 3 186 13 HOH HOH . H 5 HOH A 4 187 19 HOH HOH . H 5 HOH A 5 188 20 HOH HOH . H 5 HOH A 6 189 21 HOH HOH . H 5 HOH A 7 190 23 HOH HOH . H 5 HOH A 8 191 31 HOH HOH . H 5 HOH A 9 192 32 HOH HOH . H 5 HOH A 10 193 34 HOH HOH . H 5 HOH A 11 194 39 HOH HOH . H 5 HOH A 12 195 49 HOH HOH . H 5 HOH A 13 196 51 HOH HOH . H 5 HOH A 14 197 52 HOH HOH . H 5 HOH A 15 198 53 HOH HOH . H 5 HOH A 16 199 55 HOH HOH . H 5 HOH A 17 200 56 HOH HOH . H 5 HOH A 18 201 57 HOH HOH . H 5 HOH A 19 202 58 HOH HOH . H 5 HOH A 20 203 59 HOH HOH . H 5 HOH A 21 204 60 HOH HOH . H 5 HOH A 22 205 62 HOH HOH . H 5 HOH A 23 206 63 HOH HOH . H 5 HOH A 24 207 64 HOH HOH . H 5 HOH A 25 208 65 HOH HOH . H 5 HOH A 26 209 66 HOH HOH . H 5 HOH A 27 210 67 HOH HOH . H 5 HOH A 28 211 68 HOH HOH . H 5 HOH A 29 212 69 HOH HOH . H 5 HOH A 30 213 70 HOH HOH . H 5 HOH A 31 214 99 HOH HOH . H 5 HOH A 32 215 105 HOH HOH . H 5 HOH A 33 216 106 HOH HOH . H 5 HOH A 34 217 109 HOH HOH . H 5 HOH A 35 218 110 HOH HOH . H 5 HOH A 36 219 112 HOH HOH . H 5 HOH A 37 220 114 HOH HOH . H 5 HOH A 38 221 115 HOH HOH . H 5 HOH A 39 222 117 HOH HOH . H 5 HOH A 40 223 119 HOH HOH . H 5 HOH A 41 224 124 HOH HOH . H 5 HOH A 42 225 126 HOH HOH . H 5 HOH A 43 226 127 HOH HOH . H 5 HOH A 44 227 130 HOH HOH . H 5 HOH A 45 228 131 HOH HOH . H 5 HOH A 46 229 135 HOH HOH . H 5 HOH A 47 230 136 HOH HOH . H 5 HOH A 48 231 137 HOH HOH . H 5 HOH A 49 232 140 HOH HOH . H 5 HOH A 50 233 141 HOH HOH . H 5 HOH A 51 234 142 HOH HOH . H 5 HOH A 52 235 145 HOH HOH . I 5 HOH B 1 183 2 HOH HOH . I 5 HOH B 2 184 3 HOH HOH . I 5 HOH B 3 185 4 HOH HOH . I 5 HOH B 4 186 5 HOH HOH . I 5 HOH B 5 187 7 HOH HOH . I 5 HOH B 6 188 10 HOH HOH . I 5 HOH B 7 189 11 HOH HOH . I 5 HOH B 8 190 14 HOH HOH . I 5 HOH B 9 191 15 HOH HOH . I 5 HOH B 10 192 16 HOH HOH . I 5 HOH B 11 193 17 HOH HOH . I 5 HOH B 12 194 18 HOH HOH . I 5 HOH B 13 195 22 HOH HOH . I 5 HOH B 14 196 24 HOH HOH . I 5 HOH B 15 197 25 HOH HOH . I 5 HOH B 16 198 26 HOH HOH . I 5 HOH B 17 199 27 HOH HOH . I 5 HOH B 18 200 28 HOH HOH . I 5 HOH B 19 201 29 HOH HOH . I 5 HOH B 20 202 30 HOH HOH . I 5 HOH B 21 203 33 HOH HOH . I 5 HOH B 22 204 35 HOH HOH . I 5 HOH B 23 205 36 HOH HOH . I 5 HOH B 24 206 37 HOH HOH . I 5 HOH B 25 207 38 HOH HOH . I 5 HOH B 26 208 40 HOH HOH . I 5 HOH B 27 209 41 HOH HOH . I 5 HOH B 28 210 42 HOH HOH . I 5 HOH B 29 211 43 HOH HOH . I 5 HOH B 30 212 44 HOH HOH . I 5 HOH B 31 213 45 HOH HOH . I 5 HOH B 32 214 46 HOH HOH . I 5 HOH B 33 215 47 HOH HOH . I 5 HOH B 34 216 50 HOH HOH . I 5 HOH B 35 217 71 HOH HOH . I 5 HOH B 36 218 72 HOH HOH . I 5 HOH B 37 219 73 HOH HOH . I 5 HOH B 38 220 74 HOH HOH . I 5 HOH B 39 221 75 HOH HOH . I 5 HOH B 40 222 78 HOH HOH . I 5 HOH B 41 223 79 HOH HOH . I 5 HOH B 42 224 80 HOH HOH . I 5 HOH B 43 225 82 HOH HOH . I 5 HOH B 44 226 84 HOH HOH . I 5 HOH B 45 227 85 HOH HOH . I 5 HOH B 46 228 86 HOH HOH . I 5 HOH B 47 229 87 HOH HOH . I 5 HOH B 48 230 88 HOH HOH . I 5 HOH B 49 231 90 HOH HOH . I 5 HOH B 50 232 91 HOH HOH . I 5 HOH B 51 233 96 HOH HOH . I 5 HOH B 52 234 98 HOH HOH . I 5 HOH B 53 235 100 HOH HOH . I 5 HOH B 54 236 101 HOH HOH . I 5 HOH B 55 237 102 HOH HOH . I 5 HOH B 56 238 103 HOH HOH . I 5 HOH B 57 239 104 HOH HOH . I 5 HOH B 58 240 107 HOH HOH . I 5 HOH B 59 241 108 HOH HOH . I 5 HOH B 60 242 111 HOH HOH . I 5 HOH B 61 243 116 HOH HOH . I 5 HOH B 62 244 118 HOH HOH . I 5 HOH B 63 245 121 HOH HOH . I 5 HOH B 64 246 122 HOH HOH . I 5 HOH B 65 247 123 HOH HOH . I 5 HOH B 66 248 125 HOH HOH . I 5 HOH B 67 249 128 HOH HOH . I 5 HOH B 68 250 129 HOH HOH . I 5 HOH B 69 251 92 HOH HOH . I 5 HOH B 70 252 93 HOH HOH . I 5 HOH B 71 253 94 HOH HOH . I 5 HOH B 72 254 95 HOH HOH . I 5 HOH B 73 255 132 HOH HOH . I 5 HOH B 74 256 133 HOH HOH . I 5 HOH B 75 257 134 HOH HOH . I 5 HOH B 76 258 138 HOH HOH . I 5 HOH B 77 259 139 HOH HOH . I 5 HOH B 78 260 143 HOH HOH . I 5 HOH B 79 261 144 HOH HOH . I 5 HOH B 80 262 146 HOH HOH . I 5 HOH B 81 263 147 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 4 88.386 19.226 41.269 1 73.09 ? C1 NAG 178 B 1 HETATM 2 C C2 NAG . . . F 4 86.934 19.077 40.484 1 74.45 ? C2 NAG 178 B 1 HETATM 3 C C3 NAG . . . F 4 86.477 20.221 39.486 1 75.13 ? C3 NAG 178 B 1 HETATM 4 C C4 NAG . . . F 4 86.913 21.592 40.007 1 77.19 ? C4 NAG 178 B 1 HETATM 5 C C5 NAG . . . F 4 88.366 21.53 40.488 1 77.55 ? C5 NAG 178 B 1 HETATM 6 C C6 NAG . . . F 4 88.83 22.827 41.101 1 76.71 ? C6 NAG 178 B 1 HETATM 7 C C7 NAG . . . F 4 86.508 17.408 38.922 1 77.02 ? C7 NAG 178 B 1 HETATM 8 C C8 NAG . . . F 4 85.96 16.058 38.549 1 77.12 ? C8 NAG 178 B 1 HETATM 9 N N2 NAG . . . F 4 86.378 17.788 40.156 1 76.34 ? N2 NAG 178 B 1 HETATM 10 O O3 NAG . . . F 4 85.052 20.239 39.273 1 73.91 ? O3 NAG 178 B 1 HETATM 11 O O4 NAG . . . F 4 86.772 22.552 38.979 1 78.47 ? O4 NAG 178 B 1 HETATM 12 O O5 NAG . . . F 4 88.436 20.629 41.593 1 76.61 ? O5 NAG 178 B 1 HETATM 13 O O6 NAG . . . F 4 90.075 22.643 41.779 1 79.09 ? O6 NAG 178 B 1 HETATM 14 O O7 NAG . . . F 4 87.072 18.122 38.095 1 79.18 ? O7 NAG 178 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #