data_5AVY # _model_server_result.job_id VM9LBaPRhr0D3ZqdW3RqMA _model_server_result.datetime_utc '2024-11-08 04:31:16' _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 5avy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":4021}' # _entry.id 5AVY # _exptl.entry_id 5AVY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 10 _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 103.63 _cell.angle_gamma 90 _cell.entry_id 5AVY _cell.length_a 220.59 _cell.length_b 50.671 _cell.length_c 163.924 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AVY _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 10 _struct_asym.id L _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 C 1 NAG B 4001 NAG 4 n D NAG 2 C 2 NAG B 4002 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 B SG CYS 127 B CYS 127 1_555 B SG CYS 150 B CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 B SG CYS 160 B CYS 160 1_555 B SG CYS 176 B CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 215 B CYS 215 1_555 B SG CYS 278 B CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 B ND2 ASN 114 B ASN 114 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 B ND2 ASN 159 B ASN 159 1_555 L C1 NAG . B NAG 4021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? metalc ? metalc1 A O VAL 334 A VAL 329 1_555 H TL TL . A TL 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc2 A O ALA 335 A ALA 330 1_555 H TL TL . A TL 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc3 A O VAL 337 A VAL 332 1_555 H TL TL . A TL 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? metalc ? metalc4 A OE1 GLU 339 A GLU 334 1_555 H TL TL . A TL 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.251 ? metalc ? metalc5 A OD2 ASP 381 A ASP 376 1_555 E MG MF4 . A MF4 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc6 A OD1 ASP 381 A ASP 376 1_555 F MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc7 A O THR 383 A THR 378 1_555 F MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc8 A OD2 ASP 722 A ASP 717 1_555 F MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc9 A O LEU 730 A LEU 725 1_555 I K K . A K 2005 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.981 ? metalc ? metalc10 A O LEU 730 A LEU 725 1_555 J TL TL . A TL 2006 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.981 ? metalc ? metalc11 A O LYS 731 A LYS 726 1_555 I K K . A K 2005 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.84 ? metalc ? metalc12 A O LYS 731 A LYS 726 1_555 J TL TL . A TL 2006 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.84 ? metalc ? metalc13 A O ALA 733 A ALA 728 1_555 I K K . A K 2005 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.688 ? metalc ? metalc14 A O ALA 733 A ALA 728 1_555 J TL TL . A TL 2006 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.688 ? metalc ? metalc15 A OD1 ASP 752 A ASP 747 1_555 I K K . A K 2005 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.961 ? metalc ? metalc16 A OD1 ASP 752 A ASP 747 1_555 J TL TL . A TL 2006 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.961 ? metalc ? metalc17 A O THR 784 A THR 779 1_555 G TL TL . A TL 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc18 A OG SER 787 A SER 782 1_555 G TL TL . A TL 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc19 A OD1 ASN 788 A ASN 783 1_555 G TL TL . A TL 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? metalc ? metalc20 A OD1 ASN 788 A ASN 783 1_555 H TL TL . A TL 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.017 ? metalc ? metalc21 A OE2 GLU 791 A GLU 786 1_555 H TL TL . A TL 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? metalc ? metalc22 A OD1 ASP 816 A ASP 811 1_555 G TL TL . A TL 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.211 ? metalc ? metalc23 A OD2 ASP 816 A ASP 811 1_555 G TL TL . A TL 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc24 A OD2 ASP 816 A ASP 811 1_555 H TL TL . A TL 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc25 G TL TL . A TL 2003 1_555 M O HOH . A HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? # _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 318 n n C1 O1 NAG sing 319 n n C1 O5 NAG sing 320 n n C1 H1 NAG sing 321 n n C2 C3 NAG sing 322 n n C2 N2 NAG sing 323 n n C2 H2 NAG sing 324 n n C3 C4 NAG sing 325 n n C3 O3 NAG sing 326 n n C3 H3 NAG sing 327 n n C4 C5 NAG sing 328 n n C4 O4 NAG sing 329 n n C4 H4 NAG sing 330 n n C5 C6 NAG sing 331 n n C5 O5 NAG sing 332 n n C5 H5 NAG sing 333 n n C6 O6 NAG sing 334 n n C6 H61 NAG sing 335 n n C6 H62 NAG sing 336 n n C7 C8 NAG sing 337 n n C7 N2 NAG sing 338 n n C7 O7 NAG doub 339 n n C8 H81 NAG sing 340 n n C8 H82 NAG sing 341 n n C8 H83 NAG sing 342 n n N2 HN2 NAG sing 343 n n O1 HO1 NAG sing 344 n n O3 HO3 NAG sing 345 n n O4 HO4 NAG sing 346 n n O6 HO6 NAG sing 347 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 5AVY _atom_sites.fract_transf_matrix[1][1] 0.004533 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001099 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019735 _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] 0.006277 _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 5 MF4 A 1 2001 2001 MF4 MF4 . F 6 MG A 1 2002 2002 MG MG . G 7 TL A 1 2003 2003 TL TL . H 7 TL A 1 2004 2004 TL TL . I 8 K A 1 2005 2005 K K . J 7 TL A 1 2006 2006 TL TL . K 9 CLR B 1 3001 3001 CLR CLR . L 10 NAG B 1 4021 4021 NAG NAG . M 11 HOH A 1 2101 2101 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 . . . L 10 154.977 21.064 -49.998 1 196.66 ? C1 NAG 4021 B 1 HETATM 2 C C2 NAG . . . L 10 155.942 22.204 -50.382 1 197.34 ? C2 NAG 4021 B 1 HETATM 3 C C3 NAG . . . L 10 156.095 22.371 -51.901 1 197.44 ? C3 NAG 4021 B 1 HETATM 4 C C4 NAG . . . L 10 156.215 21.058 -52.671 1 197.46 ? C4 NAG 4021 B 1 HETATM 5 C C5 NAG . . . L 10 155.154 20.076 -52.184 1 197.34 ? C5 NAG 4021 B 1 HETATM 6 C C6 NAG . . . L 10 155.31 18.714 -52.853 1 197.41 ? C6 NAG 4021 B 1 HETATM 7 C C7 NAG . . . L 10 156.255 24.269 -49.05 1 197.68 ? C7 NAG 4021 B 1 HETATM 8 C C8 NAG . . . L 10 155.637 25.579 -48.649 1 197.67 ? C8 NAG 4021 B 1 HETATM 9 N N2 NAG . . . L 10 155.523 23.504 -49.87 1 197.52 ? N2 NAG 4021 B 1 HETATM 10 O O3 NAG . . . L 10 157.226 23.171 -52.17 1 197.59 ? O3 NAG 4021 B 1 HETATM 11 O O4 NAG . . . L 10 156.06 21.314 -54.05 1 197.45 ? O4 NAG 4021 B 1 HETATM 12 O O5 NAG . . . L 10 155.303 19.922 -50.784 1 196.98 ? O5 NAG 4021 B 1 HETATM 13 O O6 NAG . . . L 10 154.286 17.851 -52.412 1 197.49 ? O6 NAG 4021 B 1 HETATM 14 O O7 NAG . . . L 10 157.37 23.952 -48.613 1 197.72 ? O7 NAG 4021 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #