data_8XV1 # _model_server_result.job_id R8IexFMxek9Wb2xhKMVqTQ _model_server_result.datetime_utc '2024-12-03 20:35:01' _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 8xv1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":703}' # _entry.id 8XV1 # _exptl.entry_id 8XV1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 8XV1 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XV1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 G N N ? 6 H N N ? 6 I N N ? 6 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 5 5 3 MAN BMA 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 3 n C NAG 1 L 1 NAG L 1 NAG 3 n C NAG 2 L 2 NAG L 2 NAG 4 n D NAG 1 M 1 NAG M 1 NAG 4 n D NAG 2 M 2 NAG M 2 NAG 4 n D BMA 3 M 3 BMA M 3 BMA 5 n E NAG 1 N 1 NAG N 1 NAG 5 n E NAG 2 N 2 NAG N 2 NAG 5 n E BMA 3 N 3 BMA N 3 BMA 5 n E MAN 4 N 4 MAN N 4 MAN 5 n E MAN 5 N 5 MAN N 5 MAN # 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 322 A CYS 336 1_555 A SG CYS 347 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 365 A CYS 379 1_555 A SG CYS 418 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 377 A CYS 391 1_555 A SG CYS 510 A CYS 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 466 A CYS 480 1_555 A SG CYS 473 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 115 D CYS 133 1_555 B SG CYS 123 D CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 B SG CYS 326 D CYS 344 1_555 B SG CYS 343 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 512 D CYS 530 1_555 B SG CYS 524 D CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 329 A ASN 343 1_555 F C1 NAG . A NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 340 A ASN 354 1_555 G C1 NAG . A NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 B ND2 ASN 35 D ASN 53 1_555 J C1 NAG . D NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B ND2 ASN 72 D ASN 90 1_555 D C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 85 D ASN 103 1_555 E C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale6 B ND2 ASN 304 D ASN 322 1_555 H C1 NAG . D NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 B ND2 ASN 414 D ASN 432 1_555 I C1 NAG . D NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 B ND2 ASN 528 D ASN 546 1_555 C C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale9 C O4 NAG . L NAG 1 1_555 C C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale10 D O4 NAG . M NAG 1 1_555 D C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 D O4 NAG . M NAG 2 1_555 D C1 BMA . M BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 E O4 NAG . N NAG 1 1_555 E C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale13 E O4 NAG . N NAG 2 1_555 E C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 E O3 BMA . N BMA 3 1_555 E C1 MAN . N MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 E O6 BMA . N BMA 3 1_555 E C1 MAN . N MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 8XV1 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 6 NAG A 1 1301 1312 NAG NAG . G 6 NAG A 1 1302 1313 NAG NAG . H 6 NAG D 1 701 701 NAG NAG . I 6 NAG D 1 702 702 NAG NAG . J 6 NAG D 1 703 703 NAG NAG . # 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 . . . J 6 173.832 193.953 273.657 1 146.1 ? C1 NAG 703 D 1 HETATM 2 C C2 NAG . . . J 6 172.847 194.296 272.536 1 146.1 ? C2 NAG 703 D 1 HETATM 3 C C3 NAG . . . J 6 171.416 194.327 273.07 1 146.1 ? C3 NAG 703 D 1 HETATM 4 C C4 NAG . . . J 6 171.091 193.028 273.794 1 146.1 ? C4 NAG 703 D 1 HETATM 5 C C5 NAG . . . J 6 172.137 192.754 274.87 1 146.1 ? C5 NAG 703 D 1 HETATM 6 C C6 NAG . . . J 6 171.937 191.426 275.56 1 146.1 ? C6 NAG 703 D 1 HETATM 7 C C7 NAG . . . J 6 173.215 196.743 272.506 1 146.1 ? C7 NAG 703 D 1 HETATM 8 C C8 NAG . . . J 6 173.591 197.915 271.651 1 146.1 ? C8 NAG 703 D 1 HETATM 9 N N2 NAG . . . J 6 173.188 195.555 271.888 1 146.1 ? N2 NAG 703 D 1 HETATM 10 O O3 NAG . . . J 6 170.512 194.52 271.988 1 146.1 ? O3 NAG 703 D 1 HETATM 11 O O4 NAG . . . J 6 169.806 193.115 274.397 1 146.1 ? O4 NAG 703 D 1 HETATM 12 O O5 NAG . . . J 6 173.444 192.722 274.28 1 146.1 ? O5 NAG 703 D 1 HETATM 13 O O6 NAG . . . J 6 171.364 190.466 274.682 1 146.1 ? O6 NAG 703 D 1 HETATM 14 O O7 NAG . . . J 6 172.95 196.87 273.699 1 146.1 ? O7 NAG 703 D 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #