data_5C6T # _model_server_result.job_id Z_aXDGCOqnEg8GZ5fpz2FA _model_server_result.datetime_utc '2025-04-08 02:20:48' _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 5c6t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1008}' # _entry.id 5C6T # _exptl.entry_id 5C6T _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 8 _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 5C6T _cell.length_a 176.486 _cell.length_b 176.486 _cell.length_c 176.486 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C6T _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H N N ? 5 I N N ? 5 J N N ? 5 K N N ? 5 L N 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 B 1 NAG A 1009 NAG 4 n D NAG 2 B 2 NAG A 1005 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 32 A CYS 94 1_555 A SG CYS 489 A CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 49 A CYS 111 1_555 A SG CYS 445 A CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 123 A CYS 185 1_555 A SG CYS 188 A CYS 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 A SG CYS 282 A CYS 344 1_555 A SG CYS 329 A CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf5 A SG CYS 512 A CYS 574 1_555 A SG CYS 549 A CYS 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 B SG CYS 22 H CYS 22 1_555 B SG CYS 97 H CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 C SG CYS 22 L CYS 22 1_555 C SG CYS 89 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 146 A ASN 208 1_555 F C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 A ND2 ASN 219 A ASN 281 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale3 A ND2 ASN 224 A ASN 286 1_555 I C1 NAG . A NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 A ND2 ASN 240 A ASN 302 1_555 L C1 NAG . A NAG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 A ND2 ASN 279 A ASN 341 1_555 J C1 NAG . A NAG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale6 A ND2 ASN 321 A ASN 383 1_555 G C1 NAG . A NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 A ND2 ASN 343 A ASN 405 1_555 E C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 A ND2 ASN 355 A ASN 417 1_555 H C1 NAG . A NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale9 A ND2 ASN 493 A ASN 555 1_555 K C1 NAG . A NAG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale10 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? metalc ? metalc1 A OD1 ASP 447 A ASP 509 1_555 M MG MG . A MG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc2 A OD2 ASP 447 A ASP 509 1_555 M MG MG . A MG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc3 A OD1 ASP 447 A ASP 509 1_555 M MG MG . A MG 1011 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc4 A OD2 ASP 447 A ASP 509 1_555 M MG MG . A MG 1011 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 5C6T _atom_sites.fract_transf_matrix[1][1] 0.005666 _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] 0.005666 _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] 0.005666 _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 NAG A 1 1001 1001 NAG NAG . F 5 NAG A 1 1002 1002 NAG NAG . G 5 NAG A 1 1003 1003 NAG NAG . H 5 NAG A 1 1004 1004 NAG NAG . I 5 NAG A 1 1005 1006 NAG NAG . J 5 NAG A 1 1008 1007 NAG NAG . K 5 NAG A 1 1009 1008 NAG NAG . L 5 NAG A 1 1010 1100 NAG NAG . M 6 MG A 1 1011 1 MG MG . # 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 -56.509 -17.414 -60.704 1 172.82 ? C1 NAG 1008 A 1 HETATM 2 C C2 NAG . . . J 5 -57.576 -17.189 -59.61 1 181.37 ? C2 NAG 1008 A 1 HETATM 3 C C3 NAG . . . J 5 -58.917 -16.813 -60.264 1 183.64 ? C3 NAG 1008 A 1 HETATM 4 C C4 NAG . . . J 5 -58.743 -15.652 -61.235 1 184.46 ? C4 NAG 1008 A 1 HETATM 5 C C5 NAG . . . J 5 -57.65 -15.982 -62.248 1 181.25 ? C5 NAG 1008 A 1 HETATM 6 C C6 NAG . . . J 5 -57.363 -14.854 -63.21 1 179.68 ? C6 NAG 1008 A 1 HETATM 7 C C7 NAG . . . J 5 -57.674 -18.315 -57.43 1 169.51 ? C7 NAG 1008 A 1 HETATM 8 C C8 NAG . . . J 5 -57.881 -19.619 -56.718 1 157.06 ? C8 NAG 1008 A 1 HETATM 9 N N2 NAG . . . J 5 -57.736 -18.359 -58.768 1 173.64 ? N2 NAG 1008 A 1 HETATM 10 O O3 NAG . . . J 5 -59.898 -16.502 -59.279 1 174.27 ? O3 NAG 1008 A 1 HETATM 11 O O4 NAG . . . J 5 -59.963 -15.388 -61.92 1 177.31 ? O4 NAG 1008 A 1 HETATM 12 O O5 NAG . . . J 5 -56.425 -16.251 -61.551 1 176.34 ? O5 NAG 1008 A 1 HETATM 13 O O6 NAG . . . J 5 -57.223 -13.617 -62.525 1 183.24 ? O6 NAG 1008 A 1 HETATM 14 O O7 NAG . . . J 5 -57.45 -17.268 -56.827 1 172.7 ? O7 NAG 1008 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #