data_8V58 # _model_server_result.job_id KTemfJsmbQHp-EEBSRqDhA _model_server_result.datetime_utc '2024-10-11 08:26:33' _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 8v58 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 8V58 # _exptl.entry_id 8V58 _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 8V58 _cell.length_a 111.892 _cell.length_b 111.892 _cell.length_c 116.653 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8V58 _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall 'P 4w 2c' _symmetry.space_group_name_H-M 'P 41 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 'dimeric, unknown dimer interface' _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 _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 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O4 HO4 . sing 5 ? 2 6 5 GAL MAN C1 O1 . O4 HO4 . sing 6 ? 2 7 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 2 8 1 FUC NAG C1 O1 . O6 HO6 . sing 8 ? 3 2 1 IDS SGN C1 O1 . O4 HO4 . sing 9 ? 3 3 2 SGN IDS C1 O1 . O4 HO4 . sing 10 ? 3 4 3 IDS SGN C1 O1 . O4 HO4 . sing 11 ? 3 5 4 SGN IDS C1 O1 . O4 HO4 . sing 12 ? 3 6 5 IDS SGN C1 O1 . O4 HO4 . sing 13 ? 3 7 6 SGN IDS C1 O1 . O4 HO4 . sing 14 ? 3 8 7 IDS SGN C1 O1 . O4 HO4 . sing 15 ? 3 9 8 SGN IDS C1 O1 . O4 HO4 . 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 401 NAG 2 n C NAG 2 C 2 NAG A 402 NAG 2 n C BMA 3 C 3 BMA A 403 BMA 2 n C MAN 4 C 4 MAN A 404 MAN 2 n C MAN 5 C 5 MAN A 405 MAN 2 n C GAL 6 C 6 GAL A 406 GAL 2 n C MAN 7 C 7 MAN A 420 MAN 2 n C FUC 8 C 8 FUC A 410 FUC 3 n D SGN 1 D 1 SGN D 3 SGN 3 n D IDS 2 D 2 IDS D 4 IDS 3 n D SGN 3 D 3 SGN D 5 SGN 3 n D IDS 4 D 4 IDS D 6 IDS 3 n D SGN 5 D 5 SGN D 7 SGN 3 n D IDS 6 D 6 IDS D 8 IDS 3 n D SGN 7 D 7 SGN D 9 SGN 3 n D IDS 8 D 8 IDS D 10 IDS 3 n D SGN 9 D 9 SGN D 11 SGN # 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 24 A CYS 22 1_555 A SG CYS 65 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 58 A CYS 56 1_555 A SG CYS 98 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 157 A CYS 155 1_555 A SG CYS 206 A CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf4 B SG CYS 24 B CYS 22 1_555 B SG CYS 65 B CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 B SG CYS 58 B CYS 56 1_555 B SG CYS 98 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 157 B CYS 155 1_555 B SG CYS 206 B CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 101 A ASN 99 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 B ND2 ASN 101 B ASN 99 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale4 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 C O4 MAN . C MAN 4 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 C O4 MAN . C MAN 5 1_555 C C1 GAL . C GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale10 D O4 SGN . D SGN 1 1_555 D C1 IDS . D IDS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale11 D O4 IDS . D IDS 2 1_555 D C1 SGN . D SGN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale12 D O4 SGN . D SGN 3 1_555 D C1 IDS . D IDS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale13 D O4 IDS . D IDS 4 1_555 D C1 SGN . D SGN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale14 D O4 SGN . D SGN 5 1_555 D C1 IDS . D IDS 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale15 D O4 IDS . D IDS 6 1_555 D C1 SGN . D SGN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale16 D O4 SGN . D SGN 7 1_555 D C1 IDS . D IDS 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale17 D O4 IDS . D IDS 8 1_555 D C1 SGN . D SGN 9 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 368 n n C1 O1 NAG sing 369 n n C1 O5 NAG sing 370 n n C1 H1 NAG sing 371 n n C2 C3 NAG sing 372 n n C2 N2 NAG sing 373 n n C2 H2 NAG sing 374 n n C3 C4 NAG sing 375 n n C3 O3 NAG sing 376 n n C3 H3 NAG sing 377 n n C4 C5 NAG sing 378 n n C4 O4 NAG sing 379 n n C4 H4 NAG sing 380 n n C5 C6 NAG sing 381 n n C5 O5 NAG sing 382 n n C5 H5 NAG sing 383 n n C6 O6 NAG sing 384 n n C6 H61 NAG sing 385 n n C6 H62 NAG sing 386 n n C7 C8 NAG sing 387 n n C7 N2 NAG sing 388 n n C7 O7 NAG doub 389 n n C8 H81 NAG sing 390 n n C8 H82 NAG sing 391 n n C8 H83 NAG sing 392 n n N2 HN2 NAG sing 393 n n O1 HO1 NAG sing 394 n n O3 HO3 NAG sing 395 n n O4 HO4 NAG sing 396 n n O6 HO6 NAG sing 397 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 8V58 _atom_sites.fract_transf_matrix[1][1] 0.008937 _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] 0.008937 _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] 0.008572 _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 E 4 NAG B 1 401 401 NAG NAG . F 5 EDO B 1 402 1 EDO EDO . G 6 HOH B 1 501 2 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 . . . E 4 37.541 -24.807 -18.809 1 133.12 ? C1 NAG 401 B 1 HETATM 2 C C2 NAG . . . E 4 38.568 -24.252 -19.789 1 136.33 ? C2 NAG 401 B 1 HETATM 3 C C3 NAG . . . E 4 38.374 -22.748 -19.934 1 133.36 ? C3 NAG 401 B 1 HETATM 4 C C4 NAG . . . E 4 36.953 -22.454 -20.397 1 137.4 ? C4 NAG 401 B 1 HETATM 5 C C5 NAG . . . E 4 35.937 -23.093 -19.446 1 136.11 ? C5 NAG 401 B 1 HETATM 6 C C6 NAG . . . E 4 34.517 -22.983 -19.952 1 128.99 ? C6 NAG 401 B 1 HETATM 7 C C7 NAG . . . E 4 40.888 -25.15 -20.084 1 135.61 ? C7 NAG 401 B 1 HETATM 8 C C8 NAG . . . E 4 40.536 -25.557 -21.489 1 129.94 ? C8 NAG 401 B 1 HETATM 9 N N2 NAG . . . E 4 39.927 -24.554 -19.353 1 136.05 ? N2 NAG 401 B 1 HETATM 10 O O3 NAG . . . E 4 39.313 -22.219 -20.863 1 127.61 ? O3 NAG 401 B 1 HETATM 11 O O4 NAG . . . E 4 36.738 -21.048 -20.45 1 136.9 ? O4 NAG 401 B 1 HETATM 12 O O5 NAG . . . E 4 36.207 -24.496 -19.279 1 132.32 ? O5 NAG 401 B 1 HETATM 13 O O6 NAG . . . E 4 33.581 -23.307 -18.934 1 117.31 ? O6 NAG 401 B 1 HETATM 14 O O7 NAG . . . E 4 42.005 -25.355 -19.621 1 140.65 ? O7 NAG 401 B 1 HETATM 15 H H2 NAG . . . E 4 38.425 -24.669 -20.66 1 163.89 ? H2 NAG 401 B 1 HETATM 16 H H3 NAG . . . E 4 38.529 -22.322 -19.069 1 160.33 ? H3 NAG 401 B 1 HETATM 17 H H4 NAG . . . E 4 36.825 -22.829 -21.288 1 165.18 ? H4 NAG 401 B 1 HETATM 18 H H5 NAG . . . E 4 36.013 -22.659 -18.575 1 163.63 ? H5 NAG 401 B 1 HETATM 19 H H61 NAG . . . E 4 34.397 -23.596 -20.702 1 155.08 ? H61 NAG 401 B 1 HETATM 20 H H62 NAG . . . E 4 34.356 -22.07 -20.255 1 155.08 ? H62 NAG 401 B 1 HETATM 21 H H81 NAG . . . E 4 39.82 -26.22 -21.466 1 154.45 ? H81 NAG 401 B 1 HETATM 22 H H82 NAG . . . E 4 41.321 -25.94 -21.924 1 154.45 ? H82 NAG 401 B 1 HETATM 23 H H83 NAG . . . E 4 40.237 -24.774 -21.989 1 154.45 ? H83 NAG 401 B 1 HETATM 24 H HN2 NAG . . . E 4 40.147 -24.315 -18.501 1 163.55 ? HN2 NAG 401 B 1 HETATM 25 H HO3 NAG . . . E 4 39.07 -22.445 -21.687 1 153.42 ? HO3 NAG 401 B 1 HETATM 26 H HO4 NAG . . . E 4 36.102 -20.868 -21.043 1 164.57 ? HO4 NAG 401 B 1 HETATM 27 H HO6 NAG . . . E 4 33.77 -24.113 -18.611 1 141.07 ? HO6 NAG 401 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #