data_5MKF # _model_server_result.job_id 3xw-V0Lb0ENePe7Dfzn1Rw _model_server_result.datetime_utc '2025-03-06 09:15:18' _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 5mkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GA","auth_seq_id":1002}' # _entry.id 5MKF # _exptl.entry_id 5MKF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 12 _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 5MKF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MKF _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA _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 ? 3 I N N ? 3 J N N ? 3 K N N ? 3 V N N ? 3 W N N ? 3 X N N ? 3 FA N N ? 3 GA N N ? 3 HA N N ? 3 OA N N ? 3 PA N N ? 3 QA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n E NAG 1 E 1 NAG A 803 NAG 2 n E NAG 2 E 2 NAG A 804 NAG 2 n F NAG 1 F 1 NAG B 803 NAG 2 n F NAG 2 F 2 NAG B 804 NAG 2 n G NAG 1 G 1 NAG C 803 NAG 2 n G NAG 2 G 2 NAG C 804 NAG 2 n H NAG 1 H 1 NAG D 803 NAG 2 n H NAG 2 H 2 NAG D 804 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 331 A CYS 331 1_555 A SG CYS 344 A CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 B SG CYS 331 B CYS 331 1_555 B SG CYS 344 B CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 C SG CYS 331 C CYS 331 1_555 C SG CYS 344 C CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 D SG CYS 331 D CYS 331 1_555 D SG CYS 344 D CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale1 A ND2 ASN 328 A ASN 328 1_555 I C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.223 ? covale ? covale2 A ND2 ASN 362 A ASN 362 1_555 J C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.548 ? covale ? covale3 B ND2 ASN 328 B ASN 328 1_555 V C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.223 ? covale ? covale4 B ND2 ASN 362 B ASN 362 1_555 W C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.548 ? covale ? covale5 C ND2 ASN 328 C ASN 328 1_555 FA C1 NAG . C NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.223 ? covale ? covale6 C ND2 ASN 362 C ASN 362 1_555 GA C1 NAG . C NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.549 ? covale ? covale7 D ND2 ASN 328 D ASN 328 1_555 OA C1 NAG . D NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.248 ? covale ? covale8 D ND2 ASN 362 D ASN 362 1_555 PA C1 NAG . D NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.563 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale11 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? metalc ? metalc1 A OD1 ASN 681 A ASN 681 1_555 R CA CA . A CA 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc2 R CA CA . A CA 1012 1_555 B OD1 ASN 681 B ASN 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc3 R CA CA . A CA 1012 1_555 C OD1 ASN 681 C ASN 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc4 R CA CA . A CA 1012 1_555 D OD1 ASN 681 D ASN 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? # _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 271 n n C1 O1 NAG sing 272 n n C1 O5 NAG sing 273 n n C1 H1 NAG sing 274 n n C2 C3 NAG sing 275 n n C2 N2 NAG sing 276 n n C2 H2 NAG sing 277 n n C3 C4 NAG sing 278 n n C3 O3 NAG sing 279 n n C3 H3 NAG sing 280 n n C4 C5 NAG sing 281 n n C4 O4 NAG sing 282 n n C4 H4 NAG sing 283 n n C5 C6 NAG sing 284 n n C5 O5 NAG sing 285 n n C5 H5 NAG sing 286 n n C6 O6 NAG sing 287 n n C6 H61 NAG sing 288 n n C6 H62 NAG sing 289 n n C7 C8 NAG sing 290 n n C7 N2 NAG sing 291 n n C7 O7 NAG doub 292 n n C8 H81 NAG sing 293 n n C8 H82 NAG sing 294 n n C8 H83 NAG sing 295 n n N2 HN2 NAG sing 296 n n O1 HO1 NAG sing 297 n n O3 HO3 NAG sing 298 n n O4 HO4 NAG sing 299 n n O6 HO6 NAG sing 300 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 5MKF _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 I 3 NAG A 1 1001 801 NAG NAG . J 3 NAG A 1 1002 802 NAG NAG . K 3 NAG A 1 1005 800 NAG NAG . L 4 PX6 A 1 1006 7 PX6 PX6 . M 5 PLM A 1 1007 4 PLM PLM . N 5 PLM A 1 1008 5 PLM PLM . O 5 PLM A 1 1009 6 PLM PLM . P 6 CHS A 1 1010 5 CHS CHS . Q 6 CHS A 1 1011 6 CHS CHS . R 7 CA A 1 1012 4 CA CA . S 7 CA A 1 1013 5 CA CA . T 7 CA A 1 1014 6 CA CA . U 7 CA A 1 1015 7 CA CA . V 3 NAG B 1 1001 801 NAG NAG . W 3 NAG B 1 1002 802 NAG NAG . X 3 NAG B 1 1005 800 NAG NAG . Y 4 PX6 B 1 1006 8 PX6 PX6 . Z 5 PLM B 1 1007 7 PLM PLM . AA 5 PLM B 1 1008 8 PLM PLM . BA 5 PLM B 1 1009 9 PLM PLM . CA 6 CHS B 1 1010 7 CHS CHS . DA 6 CHS B 1 1011 8 CHS CHS . EA 7 CA B 1 1012 2 CA CA . FA 3 NAG C 1 1001 801 NAG NAG . GA 3 NAG C 1 1002 802 NAG NAG . HA 3 NAG C 1 1005 800 NAG NAG . IA 4 PX6 C 1 1006 9 PX6 PX6 . JA 5 PLM C 1 1007 10 PLM PLM . KA 5 PLM C 1 1008 11 PLM PLM . LA 5 PLM C 1 1009 12 PLM PLM . MA 6 CHS C 1 1010 9 CHS CHS . NA 6 CHS C 1 1011 10 CHS CHS . OA 3 NAG D 1 1001 801 NAG NAG . PA 3 NAG D 1 1002 802 NAG NAG . QA 3 NAG D 1 1005 800 NAG NAG . RA 4 PX6 D 1 1006 10 PX6 PX6 . SA 5 PLM D 1 1007 13 PLM PLM . TA 5 PLM D 1 1008 14 PLM PLM . UA 5 PLM D 1 1009 15 PLM PLM . VA 6 CHS D 1 1010 3 CHS CHS . WA 6 CHS D 1 1011 4 CHS CHS . # 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 . . . GA 3 93.405 136.913 136.467 1 94.88 ? C1 NAG 1002 C 1 HETATM 2 C C2 NAG . . . GA 3 92.514 135.698 136.175 1 94.88 ? C2 NAG 1002 C 1 HETATM 3 C C3 NAG . . . GA 3 92.034 135.069 137.485 1 94.88 ? C3 NAG 1002 C 1 HETATM 4 C C4 NAG . . . GA 3 93.201 134.807 138.435 1 94.88 ? C4 NAG 1002 C 1 HETATM 5 C C5 NAG . . . GA 3 94.067 136.058 138.592 1 94.88 ? C5 NAG 1002 C 1 HETATM 6 C C6 NAG . . . GA 3 95.314 135.822 139.411 1 94.88 ? C6 NAG 1002 C 1 HETATM 7 C C7 NAG . . . GA 3 90.134 135.669 135.58 1 94.88 ? C7 NAG 1002 C 1 HETATM 8 C C8 NAG . . . GA 3 89.092 136.148 134.616 1 94.88 ? C8 NAG 1002 C 1 HETATM 9 N N2 NAG . . . GA 3 91.386 136.07 135.338 1 94.88 ? N2 NAG 1002 C 1 HETATM 10 O O3 NAG . . . GA 3 91.365 133.844 137.203 1 94.88 ? O3 NAG 1002 C 1 HETATM 11 O O4 NAG . . . GA 3 92.703 134.424 139.712 1 94.88 ? O4 NAG 1002 C 1 HETATM 12 O O5 NAG . . . GA 3 94.5 136.516 137.302 1 94.88 ? O5 NAG 1002 C 1 HETATM 13 O O6 NAG . . . GA 3 95.071 134.915 140.479 1 94.88 ? O6 NAG 1002 C 1 HETATM 14 O O7 NAG . . . GA 3 89.853 134.954 136.539 1 94.88 ? O7 NAG 1002 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 202 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #