data_7LF9 # _model_server_result.job_id MhcwhRrQszxnRc_aC-b8rA _model_server_result.datetime_utc '2024-12-25 04:33:17' _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 7lf9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 7LF9 # _exptl.entry_id 7LF9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _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 7LF9 _cell.length_a 49.478 _cell.length_b 77.964 _cell.length_c 140.492 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LF9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 _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 F _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 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 3 MAN BMA C1 O1 . O3 HO3 . sing 6 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 8 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 9 ? 3 5 4 NAG MAN C1 O1 . O2 HO2 . sing 10 ? 3 6 5 GAL NAG C1 O1 . O4 HO4 . sing 11 ? 3 7 3 MAN BMA C1 O1 . O3 HO3 . 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 444 NAG 2 n C NAG 2 C 2 NAG A 445 NAG 2 n C BMA 3 C 3 BMA A 446 BMA 2 n C MAN 4 C 4 MAN A 449 MAN 2 n C NAG 5 C 5 NAG A 450 NAG 2 n C MAN 6 C 6 MAN A 448 MAN 3 n D NAG 1 D 1 NAG B 444 NAG 3 n D NAG 2 D 2 NAG B 445 NAG 3 n D BMA 3 D 3 BMA B 446 BMA 3 n D MAN 4 D 4 MAN B 451 MAN 3 n D NAG 5 D 5 NAG B 452 NAG 3 n D GAL 6 D 6 GAL B 453 GAL 3 n D MAN 7 D 7 MAN B 447 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 47 A CYS 261 1_555 A SG CYS 107 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf2 A SG CYS 153 A CYS 367 1_555 A SG CYS 211 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 B SG CYS 47 B CYS 261 1_555 B SG CYS 107 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 B SG CYS 153 B CYS 367 1_555 B SG CYS 211 B CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A ND2 ASN 83 A ASN 297 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 115 A ASN 329 1_555 F C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale3 B ND2 ASN 83 B ASN 297 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale6 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 C O2 MAN . C MAN 4 1_555 C C1 NAG . C NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale11 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale12 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale13 D O2 MAN . D MAN 4 1_555 D C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale14 D O4 NAG . D NAG 5 1_555 D C1 GAL . D GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 332 n n C1 O1 NAG sing 333 n n C1 O5 NAG sing 334 n n C1 H1 NAG sing 335 n n C2 C3 NAG sing 336 n n C2 N2 NAG sing 337 n n C2 H2 NAG sing 338 n n C3 C4 NAG sing 339 n n C3 O3 NAG sing 340 n n C3 H3 NAG sing 341 n n C4 C5 NAG sing 342 n n C4 O4 NAG sing 343 n n C4 H4 NAG sing 344 n n C5 C6 NAG sing 345 n n C5 O5 NAG sing 346 n n C5 H5 NAG sing 347 n n C6 O6 NAG sing 348 n n C6 H61 NAG sing 349 n n C6 H62 NAG sing 350 n n C7 C8 NAG sing 351 n n C7 N2 NAG sing 352 n n C7 O7 NAG doub 353 n n C8 H81 NAG sing 354 n n C8 H82 NAG sing 355 n n C8 H83 NAG sing 356 n n N2 HN2 NAG sing 357 n n O1 HO1 NAG sing 358 n n O3 HO3 NAG sing 359 n n O4 HO4 NAG sing 360 n n O6 HO6 NAG sing 361 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 7LF9 _atom_sites.fract_transf_matrix[1][1] 0.020211 _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] 0.012826 _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] 0.007118 _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 FUC A 1 501 447 FUC FUC . F 5 NAG A 1 502 451 NAG NAG . G 4 FUC B 1 501 450 FUC FUC . H 6 HOH A 1 601 24 HOH HOH . H 6 HOH A 2 602 5 HOH HOH . H 6 HOH A 3 603 10 HOH HOH . H 6 HOH A 4 604 28 HOH HOH . H 6 HOH A 5 605 23 HOH HOH . H 6 HOH A 6 606 15 HOH HOH . H 6 HOH A 7 607 32 HOH HOH . H 6 HOH A 8 608 17 HOH HOH . H 6 HOH A 9 609 8 HOH HOH . H 6 HOH A 10 610 9 HOH HOH . H 6 HOH A 11 611 19 HOH HOH . H 6 HOH A 12 612 4 HOH HOH . H 6 HOH A 13 613 25 HOH HOH . I 6 HOH B 1 601 12 HOH HOH . I 6 HOH B 2 602 13 HOH HOH . I 6 HOH B 3 603 30 HOH HOH . I 6 HOH B 4 604 22 HOH HOH . I 6 HOH B 5 605 20 HOH HOH . I 6 HOH B 6 606 27 HOH HOH . I 6 HOH B 7 607 6 HOH HOH . I 6 HOH B 8 608 16 HOH HOH . I 6 HOH B 9 609 3 HOH HOH . I 6 HOH B 10 610 11 HOH HOH . I 6 HOH B 11 611 2 HOH HOH . I 6 HOH B 12 612 31 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 . . . F 5 2.425 7.088 -8.305 1 149.33 ? C1 NAG 502 A 1 HETATM 2 C C2 NAG . . . F 5 2.432 5.734 -9.055 1 155.24 ? C2 NAG 502 A 1 HETATM 3 C C3 NAG . . . F 5 1.027 5.124 -9.063 1 157.35 ? C3 NAG 502 A 1 HETATM 4 C C4 NAG . . . F 5 0.478 5.025 -7.646 1 156.02 ? C4 NAG 502 A 1 HETATM 5 C C5 NAG . . . F 5 0.51 6.393 -6.97 1 153.78 ? C5 NAG 502 A 1 HETATM 6 C C6 NAG . . . F 5 0.069 6.339 -5.519 1 154.11 ? C6 NAG 502 A 1 HETATM 7 C C7 NAG . . . F 5 3.346 4.861 -11.18 1 158.67 ? C7 NAG 502 A 1 HETATM 8 C C8 NAG . . . F 5 3.831 5.218 -12.557 1 152.05 ? C8 NAG 502 A 1 HETATM 9 N N2 NAG . . . F 5 2.934 5.884 -10.417 1 158.36 ? N2 NAG 502 A 1 HETATM 10 O O3 NAG . . . F 5 1.063 3.819 -9.64 1 158.34 ? O3 NAG 502 A 1 HETATM 11 O O4 NAG . . . F 5 -0.864 4.545 -7.683 1 156.79 ? O4 NAG 502 A 1 HETATM 12 O O5 NAG . . . F 5 1.852 6.91 -6.974 1 151.27 ? O5 NAG 502 A 1 HETATM 13 O O6 NAG . . . F 5 0.543 5.163 -4.87 1 153.34 ? O6 NAG 502 A 1 HETATM 14 O O7 NAG . . . F 5 3.325 3.698 -10.78 1 159.88 ? O7 NAG 502 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 41 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #