data_3O9W # _model_server_result.job_id pSgeA14kCbHAcDDAuYEdPQ _model_server_result.datetime_utc '2024-10-30 09:20:56' _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 3o9w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 3O9W # _exptl.entry_id 3O9W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _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 3O9W _cell.length_a 78.003 _cell.length_b 188.368 _cell.length_c 149.791 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3O9W _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _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 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 1 FUC NAG C1 O1 . O6 HO6 . 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 5 n E NAG 1 E 1 NAG E 502 NAG 5 n E NAG 2 E 2 NAG E 503 NAG 6 n F NAG 1 F 1 NAG E 504 NAG 6 n F NAG 2 F 2 NAG E 505 NAG 6 n F FUC 3 F 3 FUC E 506 FUC # 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 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf2 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 C SG CYS 24 C CYS 22 1_555 C SG CYS 91 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf4 C SG CYS 138 C CYS 139 1_555 C SG CYS 188 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf5 C SG CYS 163 C CYS 164 1_555 D SG CYS 169 D CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf6 D SG CYS 24 D CYS 23 1_555 D SG CYS 92 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf7 D SG CYS 143 D CYS 142 1_555 D SG CYS 208 D CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 G C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? # _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 393 n n C1 O1 NAG sing 394 n n C1 O5 NAG sing 395 n n C1 H1 NAG sing 396 n n C2 C3 NAG sing 397 n n C2 N2 NAG sing 398 n n C2 H2 NAG sing 399 n n C3 C4 NAG sing 400 n n C3 O3 NAG sing 401 n n C3 H3 NAG sing 402 n n C4 C5 NAG sing 403 n n C4 O4 NAG sing 404 n n C4 H4 NAG sing 405 n n C5 C6 NAG sing 406 n n C5 O5 NAG sing 407 n n C5 H5 NAG sing 408 n n C6 O6 NAG sing 409 n n C6 H61 NAG sing 410 n n C6 H62 NAG sing 411 n n C7 C8 NAG sing 412 n n C7 N2 NAG sing 413 n n C7 O7 NAG doub 414 n n C8 H81 NAG sing 415 n n C8 H82 NAG sing 416 n n C8 H83 NAG sing 417 n n N2 HN2 NAG sing 418 n n O1 HO1 NAG sing 419 n n O3 HO3 NAG sing 420 n n O4 HO4 NAG sing 421 n n O6 HO6 NAG sing 422 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 3O9W _atom_sites.fract_transf_matrix[1][1] 0.01282 _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] 0.005309 _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] 0.006676 _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 G 7 NAG A 1 501 501 NAG NAG . H 8 1O2 A 1 507 507 1O2 1O2 . I 9 HOH A 1 286 26 HOH HOH . I 9 HOH A 2 287 30 HOH HOH . I 9 HOH A 3 288 31 HOH HOH . I 9 HOH A 4 289 40 HOH HOH . I 9 HOH A 5 290 41 HOH HOH . I 9 HOH A 6 291 42 HOH HOH . I 9 HOH A 7 292 43 HOH HOH . I 9 HOH A 8 293 51 HOH HOH . I 9 HOH A 9 294 64 HOH HOH . I 9 HOH A 10 295 84 HOH HOH . I 9 HOH A 11 296 88 HOH HOH . I 9 HOH A 12 297 95 HOH HOH . J 9 HOH B 1 100 1 HOH HOH . J 9 HOH B 2 101 2 HOH HOH . J 9 HOH B 3 102 4 HOH HOH . J 9 HOH B 4 103 49 HOH HOH . J 9 HOH B 5 104 67 HOH HOH . J 9 HOH B 6 105 68 HOH HOH . J 9 HOH B 7 106 74 HOH HOH . K 9 HOH C 1 61 61 HOH HOH . K 9 HOH C 2 211 7 HOH HOH . K 9 HOH C 3 212 9 HOH HOH . K 9 HOH C 4 213 13 HOH HOH . K 9 HOH C 5 214 14 HOH HOH . K 9 HOH C 6 215 17 HOH HOH . K 9 HOH C 7 216 21 HOH HOH . K 9 HOH C 8 217 36 HOH HOH . K 9 HOH C 9 218 37 HOH HOH . K 9 HOH C 10 219 46 HOH HOH . K 9 HOH C 11 220 73 HOH HOH . K 9 HOH C 12 221 82 HOH HOH . K 9 HOH C 13 222 85 HOH HOH . K 9 HOH C 14 223 89 HOH HOH . K 9 HOH C 15 224 98 HOH HOH . K 9 HOH C 16 225 99 HOH HOH . K 9 HOH C 17 226 100 HOH HOH . L 9 HOH D 1 241 3 HOH HOH . L 9 HOH D 2 242 5 HOH HOH . L 9 HOH D 3 243 11 HOH HOH . L 9 HOH D 4 244 15 HOH HOH . L 9 HOH D 5 245 16 HOH HOH . L 9 HOH D 6 246 18 HOH HOH . L 9 HOH D 7 247 20 HOH HOH . L 9 HOH D 8 248 35 HOH HOH . L 9 HOH D 9 249 45 HOH HOH . L 9 HOH D 10 250 47 HOH HOH . L 9 HOH D 11 251 54 HOH HOH . L 9 HOH D 12 252 62 HOH HOH . L 9 HOH D 13 253 63 HOH HOH . L 9 HOH D 14 254 70 HOH HOH . L 9 HOH D 15 255 86 HOH HOH . L 9 HOH D 16 256 90 HOH HOH . L 9 HOH D 17 257 94 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 . . . G 7 -31.649 -41.503 18.875 1 70.88 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . G 7 -30.773 -42.765 19.073 1 78.09 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . G 7 -29.584 -42.592 20.037 1 79.76 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . G 7 -28.838 -41.303 19.715 1 76.31 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . G 7 -29.844 -40.179 19.935 1 72.04 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . G 7 -29.202 -38.789 19.894 1 68.99 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . G 7 -32.232 -44.694 18.637 1 83.47 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . G 7 -33.062 -45.779 19.255 1 86.42 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . G 7 -31.609 -43.881 19.501 1 82.06 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . G 7 -28.69 -43.686 19.954 1 83.62 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . G 7 -27.688 -41.153 20.522 1 78.37 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . G 7 -30.894 -40.286 18.97 1 70.07 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . G 7 -28.464 -38.601 18.705 1 69.04 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . G 7 -32.162 -44.586 17.405 1 82.28 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #