data_5BO8 # _model_server_result.job_id YzHrzV9inq7XwaVbNG0o1g _model_server_result.datetime_utc '2024-11-22 07:33:28' _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 5bo8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":405}' # _entry.id 5BO8 # _exptl.entry_id 5BO8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 5BO8 _cell.length_a 88.17 _cell.length_b 94.22 _cell.length_c 126.19 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BO8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,J,K,L,M _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 5 _struct_asym.id J _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 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 4 4 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 2 n C NAG 1 C 1 NAG A 508 NAG 2 n C NAG 2 C 2 NAG A 509 NAG 2 n D NAG 1 D 1 NAG A 518 NAG 2 n D NAG 2 D 2 NAG A 519 NAG 2 n E NAG 1 E 1 NAG A 528 NAG 2 n E NAG 2 E 2 NAG A 529 NAG 3 n F NAG 1 F 1 NAG A 538 NAG 3 n F NAG 2 F 2 NAG A 539 NAG 3 n F BMA 3 F 3 BMA A 540 BMA 3 n F MAN 4 F 4 MAN A 541 MAN 4 n G NAG 1 G 1 NAG B 508 NAG 4 n G NAG 2 G 2 NAG B 509 NAG 4 n G BMA 3 G 3 BMA B 510 BMA 4 n G FUC 4 G 4 FUC B 512 FUC 2 n H NAG 1 H 1 NAG B 528 NAG 2 n H NAG 2 H 2 NAG B 529 NAG 2 n I NAG 1 I 1 NAG B 538 NAG 2 n I NAG 2 I 2 NAG B 539 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 125 A CYS 162 1_555 A SG CYS 276 A CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? disulf ? disulf2 A SG CYS 139 A CYS 176 1_555 A SG CYS 342 A CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? disulf ? disulf3 B SG CYS 125 B CYS 162 1_555 B SG CYS 276 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? disulf ? disulf4 B SG CYS 139 B CYS 176 1_555 B SG CYS 342 B CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? covale ? covale1 A ND2 ASN 56 A ASN 93 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 76 A ASN 113 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale3 A ND2 ASN 123 A ASN 160 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 A ND2 ASN 169 A ASN 206 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale5 B ND2 ASN 56 B ASN 93 1_555 J C1 NAG . B NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale6 B ND2 ASN 76 B ASN 113 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B ND2 ASN 123 B ASN 160 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale8 B ND2 ASN 169 B ASN 206 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale13 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale14 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale15 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale16 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale17 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale19 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _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 328 n n C1 O1 NAG sing 329 n n C1 O5 NAG sing 330 n n C1 H1 NAG sing 331 n n C2 C3 NAG sing 332 n n C2 N2 NAG sing 333 n n C2 H2 NAG sing 334 n n C3 C4 NAG sing 335 n n C3 O3 NAG sing 336 n n C3 H3 NAG sing 337 n n C4 C5 NAG sing 338 n n C4 O4 NAG sing 339 n n C4 H4 NAG sing 340 n n C5 C6 NAG sing 341 n n C5 O5 NAG sing 342 n n C5 H5 NAG sing 343 n n C6 O6 NAG sing 344 n n C6 H61 NAG sing 345 n n C6 H62 NAG sing 346 n n C7 C8 NAG sing 347 n n C7 N2 NAG sing 348 n n C7 O7 NAG doub 349 n n C8 H81 NAG sing 350 n n C8 H82 NAG sing 351 n n C8 H83 NAG sing 352 n n N2 HN2 NAG sing 353 n n O1 HO1 NAG sing 354 n n O3 HO3 NAG sing 355 n n O4 HO4 NAG sing 356 n n O6 HO6 NAG sing 357 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 5BO8 _atom_sites.fract_transf_matrix[1][1] 0.011342 _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] 0.010613 _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] 0.007925 _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 J 5 NAG B 1 405 518 NAG NAG . K 6 CIT B 1 410 1 CIT CIT . L 7 HOH A 1 501 19 HOH HOH . L 7 HOH A 2 502 14 HOH HOH . L 7 HOH A 3 503 5 HOH HOH . L 7 HOH A 4 504 29 HOH HOH . L 7 HOH A 5 505 22 HOH HOH . L 7 HOH A 6 506 72 HOH HOH . L 7 HOH A 7 507 2 HOH HOH . L 7 HOH A 8 508 47 HOH HOH . L 7 HOH A 9 509 34 HOH HOH . L 7 HOH A 10 510 27 HOH HOH . L 7 HOH A 11 511 79 HOH HOH . L 7 HOH A 12 512 54 HOH HOH . L 7 HOH A 13 513 8 HOH HOH . L 7 HOH A 14 514 35 HOH HOH . L 7 HOH A 15 515 69 HOH HOH . L 7 HOH A 16 516 16 HOH HOH . L 7 HOH A 17 517 11 HOH HOH . L 7 HOH A 18 518 80 HOH HOH . L 7 HOH A 19 519 9 HOH HOH . L 7 HOH A 20 520 15 HOH HOH . L 7 HOH A 21 521 38 HOH HOH . L 7 HOH A 22 522 63 HOH HOH . L 7 HOH A 23 523 39 HOH HOH . L 7 HOH A 24 524 51 HOH HOH . L 7 HOH A 25 525 75 HOH HOH . L 7 HOH A 26 526 24 HOH HOH . L 7 HOH A 27 527 62 HOH HOH . L 7 HOH A 28 528 28 HOH HOH . L 7 HOH A 29 529 20 HOH HOH . L 7 HOH A 30 530 7 HOH HOH . L 7 HOH A 31 531 30 HOH HOH . L 7 HOH A 32 532 37 HOH HOH . L 7 HOH A 33 533 87 HOH HOH . L 7 HOH A 34 534 61 HOH HOH . L 7 HOH A 35 535 26 HOH HOH . M 7 HOH B 1 501 56 HOH HOH . M 7 HOH B 2 502 36 HOH HOH . M 7 HOH B 3 503 31 HOH HOH . M 7 HOH B 4 504 52 HOH HOH . M 7 HOH B 5 505 18 HOH HOH . M 7 HOH B 6 506 21 HOH HOH . M 7 HOH B 7 507 1 HOH HOH . M 7 HOH B 8 508 25 HOH HOH . M 7 HOH B 9 509 4 HOH HOH . M 7 HOH B 10 510 6 HOH HOH . M 7 HOH B 11 511 13 HOH HOH . M 7 HOH B 12 512 3 HOH HOH . M 7 HOH B 13 513 53 HOH HOH . M 7 HOH B 14 514 55 HOH HOH . M 7 HOH B 15 515 71 HOH HOH . M 7 HOH B 16 516 32 HOH HOH . M 7 HOH B 17 517 50 HOH HOH . M 7 HOH B 18 518 17 HOH HOH . M 7 HOH B 19 519 42 HOH HOH . M 7 HOH B 20 520 77 HOH HOH . M 7 HOH B 21 521 46 HOH HOH . M 7 HOH B 22 522 45 HOH HOH . M 7 HOH B 23 523 57 HOH HOH . M 7 HOH B 24 524 33 HOH HOH . M 7 HOH B 25 525 66 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 . . . J 5 81.372 51.686 21.478 1 86.5 ? C1 NAG 405 B 1 HETATM 2 C C2 NAG . . . J 5 81.252 50.234 20.894 1 92.31 ? C2 NAG 405 B 1 HETATM 3 C C3 NAG . . . J 5 81.73 50.149 19.4 1 97.2 ? C3 NAG 405 B 1 HETATM 4 C C4 NAG . . . J 5 81.07 51.248 18.58 1 93.69 ? C4 NAG 405 B 1 HETATM 5 C C5 NAG . . . J 5 81.488 52.56 19.232 1 93.34 ? C5 NAG 405 B 1 HETATM 6 C C6 NAG . . . J 5 81.078 53.867 18.581 1 90.23 ? C6 NAG 405 B 1 HETATM 7 C C7 NAG . . . J 5 83.153 48.775 21.81 1 98.09 ? C7 NAG 405 B 1 HETATM 8 C C8 NAG . . . J 5 83.491 47.57 22.658 1 86.59 ? C8 NAG 405 B 1 HETATM 9 N N2 NAG . . . J 5 81.843 49.128 21.691 1 94.64 ? N2 NAG 405 B 1 HETATM 10 O O3 NAG . . . J 5 81.498 48.897 18.705 1 96.62 ? O3 NAG 405 B 1 HETATM 11 O O4 NAG . . . J 5 81.468 51.135 17.216 1 98.26 ? O4 NAG 405 B 1 HETATM 12 O O5 NAG . . . J 5 80.82 52.541 20.478 1 100.48 ? O5 NAG 405 B 1 HETATM 13 O O6 NAG . . . J 5 81.747 54.881 19.347 1 79.92 ? O6 NAG 405 B 1 HETATM 14 O O7 NAG . . . J 5 84.073 49.382 21.286 1 111.95 ? O7 NAG 405 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #