data_8SD2 # _model_server_result.job_id gumiFbOxkiFsZMRUzloAAg _model_server_result.datetime_utc '2024-10-17 17:42:02' _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 8sd2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8SD2 # _exptl.entry_id 8SD2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _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 8SD2 _cell.length_a 166.638 _cell.length_b 166.638 _cell.length_c 166.638 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SD2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 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 ? 4 D N N ? 4 E N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 3 n C NAG 1 C 1 NAG C 1 NAG 3 n C NAG 2 C 2 NAG C 2 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 5 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 A SG CYS 43 A CYS 52 1_555 A SG CYS 275 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf3 A SG CYS 56 A CYS 64 1_555 A SG CYS 68 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 136 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf5 A SG CYS 279 A CYS 281 1_555 A SG CYS 303 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? covale ? covale1 A ND2 ASN 12 A ASN 21 1_555 E C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 24 A ASN 33 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 A ND2 ASN 287 A ASN 289 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? # _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 297 n n C1 O1 NAG sing 298 n n C1 O5 NAG sing 299 n n C1 H1 NAG sing 300 n n C2 C3 NAG sing 301 n n C2 N2 NAG sing 302 n n C2 H2 NAG sing 303 n n C3 C4 NAG sing 304 n n C3 O3 NAG sing 305 n n C3 H3 NAG sing 306 n n C4 C5 NAG sing 307 n n C4 O4 NAG sing 308 n n C4 H4 NAG sing 309 n n C5 C6 NAG sing 310 n n C5 O5 NAG sing 311 n n C5 H5 NAG sing 312 n n C6 O6 NAG sing 313 n n C6 H61 NAG sing 314 n n C6 H62 NAG sing 315 n n C7 C8 NAG sing 316 n n C7 N2 NAG sing 317 n n C7 O7 NAG doub 318 n n C8 H81 NAG sing 319 n n C8 H82 NAG sing 320 n n C8 H83 NAG sing 321 n n N2 HN2 NAG sing 322 n n O1 HO1 NAG sing 323 n n O3 HO3 NAG sing 324 n n O4 HO4 NAG sing 325 n n O6 HO6 NAG sing 326 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 8SD2 _atom_sites.fract_transf_matrix[1][1] 0.006001 _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] 0.006001 _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] 0.006001 _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 4 NAG A 1 401 326 NAG NAG . E 4 NAG A 1 402 328 NAG NAG . F 5 NO3 A 1 403 331 NO3 NO3 . G 6 FIE B 1 201 1 FIE FIE . H 7 HOH A 1 501 16 HOH HOH . H 7 HOH A 2 502 2 HOH HOH . H 7 HOH A 3 503 31 HOH HOH . H 7 HOH A 4 504 33 HOH HOH . H 7 HOH A 5 505 24 HOH HOH . H 7 HOH A 6 506 21 HOH HOH . H 7 HOH A 7 507 6 HOH HOH . H 7 HOH A 8 508 37 HOH HOH . H 7 HOH A 9 509 13 HOH HOH . H 7 HOH A 10 510 18 HOH HOH . H 7 HOH A 11 511 20 HOH HOH . H 7 HOH A 12 512 39 HOH HOH . H 7 HOH A 13 513 4 HOH HOH . H 7 HOH A 14 514 25 HOH HOH . H 7 HOH A 15 515 28 HOH HOH . H 7 HOH A 16 516 7 HOH HOH . H 7 HOH A 17 517 38 HOH HOH . H 7 HOH A 18 518 1 HOH HOH . H 7 HOH A 19 519 10 HOH HOH . H 7 HOH A 20 520 34 HOH HOH . H 7 HOH A 21 521 40 HOH HOH . H 7 HOH A 22 522 5 HOH HOH . H 7 HOH A 23 523 8 HOH HOH . H 7 HOH A 24 524 26 HOH HOH . H 7 HOH A 25 525 22 HOH HOH . H 7 HOH A 26 526 9 HOH HOH . H 7 HOH A 27 527 29 HOH HOH . H 7 HOH A 28 528 11 HOH HOH . H 7 HOH A 29 529 14 HOH HOH . H 7 HOH A 30 530 32 HOH HOH . H 7 HOH A 31 531 17 HOH HOH . H 7 HOH A 32 532 15 HOH HOH . H 7 HOH A 33 533 30 HOH HOH . H 7 HOH A 34 534 19 HOH HOH . H 7 HOH A 35 535 27 HOH HOH . H 7 HOH A 36 536 3 HOH HOH . H 7 HOH A 37 537 41 HOH HOH . H 7 HOH A 38 538 12 HOH HOH . I 7 HOH B 1 301 35 HOH HOH . I 7 HOH B 2 302 36 HOH HOH . I 7 HOH B 3 303 23 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 . . . D 4 -31.873 10.709 -18.66 1 133.14 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . D 4 -32.896 11.828 -18.858 1 134.82 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . D 4 -32.189 13.177 -19.014 1 134.78 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . D 4 -31.29 13.434 -17.807 1 139.88 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . D 4 -30.285 12.281 -17.67 1 144.5 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . D 4 -29.373 12.444 -16.45 1 141.53 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . D 4 -33.376 11.213 -21.203 1 121.06 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . D 4 -34.446 10.785 -22.172 1 107.46 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . D 4 -33.794 11.503 -19.961 1 122.54 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . D 4 -33.165 14.211 -19.1 1 140.12 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . D 4 -30.641 14.707 -17.921 1 131.31 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . D 4 -31.004 11.041 -17.554 1 148.76 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . D 4 -28.076 12.916 -16.835 1 128.92 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . D 4 -32.2 11.26 -21.541 1 117.42 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #