data_8TP9 # _model_server_result.job_id TtB36UYMmUweII4-4hf3sg _model_server_result.datetime_utc '2025-03-05 18:48:43' _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 8tp9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":502}' # _entry.id 8TP9 # _exptl.entry_id 8TP9 _exptl.method 'ELECTRON MICROSCOPY' # _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 9 _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 8TP9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TP9 _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 ? _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,N,O,P,Q,R,S,T,U _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T N N ? 5 U 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 J NAG 1 I 1 NAG A 499 NAG 4 n J NAG 2 I 2 NAG A 500 NAG 4 n K NAG 1 J 1 NAG B 499 NAG 4 n K NAG 2 J 2 NAG B 500 NAG 4 n L NAG 1 K 1 NAG C 499 NAG 4 n L NAG 2 K 2 NAG C 500 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 19 A CYS 14 1_555 A SG CYS 477 A CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 57 A CYS 52 1_555 A SG CYS 288 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 70 A CYS 64 1_555 A SG CYS 82 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf4 A SG CYS 105 A CYS 97 1_555 A SG CYS 149 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 292 A CYS 281 1_555 A SG CYS 316 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 A SG CYS 484 A CYS 473 1_555 A SG CYS 488 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 B SG CYS 19 B CYS 14 1_555 B SG CYS 477 B CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 B SG CYS 57 B CYS 52 1_555 B SG CYS 288 B CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf9 B SG CYS 70 B CYS 64 1_555 B SG CYS 82 B CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf10 B SG CYS 105 B CYS 97 1_555 B SG CYS 149 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 292 B CYS 281 1_555 B SG CYS 316 B CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf12 B SG CYS 484 B CYS 473 1_555 B SG CYS 488 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 C SG CYS 19 C CYS 14 1_555 C SG CYS 477 C CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf14 C SG CYS 57 C CYS 52 1_555 C SG CYS 288 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf15 C SG CYS 70 C CYS 64 1_555 C SG CYS 82 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf16 C SG CYS 105 C CYS 97 1_555 C SG CYS 149 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf17 C SG CYS 292 C CYS 281 1_555 C SG CYS 316 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf18 C SG CYS 484 C CYS 473 1_555 C SG CYS 488 C CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf19 D SG CYS 22 D CYS 22 1_555 D SG CYS 97 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf20 E SG CYS 22 E CYS 22 1_555 E SG CYS 97 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf21 F SG CYS 23 F CYS 23 1_555 F SG CYS 88 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf22 G SG CYS 23 G CYS 23 1_555 G SG CYS 88 G CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf23 H SG CYS 22 H CYS 22 1_555 H SG CYS 97 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf24 I SG CYS 23 L CYS 23 1_555 I SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? covale ? covale1 A ND2 ASN 38 A ASN 33 1_555 N C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.524 ? covale ? covale2 A ND2 ASN 179 A ASN 169 1_555 J C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.525 ? covale ? covale3 A ND2 ASN 300 A ASN 289 1_555 O C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale4 A ND2 ASN 494 A ASN 483 1_555 M C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? covale ? covale5 B ND2 ASN 38 B ASN 33 1_555 Q C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.524 ? covale ? covale6 B ND2 ASN 179 B ASN 169 1_555 K C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.525 ? covale ? covale7 B ND2 ASN 300 B ASN 289 1_555 R C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale8 B ND2 ASN 494 B ASN 483 1_555 P C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? covale ? covale9 C ND2 ASN 38 C ASN 33 1_555 T C1 NAG . C NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.524 ? covale ? covale10 C ND2 ASN 179 C ASN 169 1_555 L C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.524 ? covale ? covale11 C ND2 ASN 300 C ASN 289 1_555 U C1 NAG . C NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale12 C ND2 ASN 494 C ASN 483 1_555 S C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.523 ? covale ? covale13 J O4 NAG . I NAG 1 1_555 J C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? covale ? covale14 K O4 NAG . J NAG 1 1_555 K C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? covale ? covale15 L O4 NAG . K NAG 1 1_555 L C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? # _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 8TP9 _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 M 5 NAG A 1 501 496 NAG NAG . N 5 NAG A 1 502 498 NAG NAG . O 5 NAG A 1 503 501 NAG NAG . P 5 NAG B 1 501 496 NAG NAG . Q 5 NAG B 1 502 498 NAG NAG . R 5 NAG B 1 503 501 NAG NAG . S 5 NAG C 1 501 496 NAG NAG . T 5 NAG C 1 502 498 NAG NAG . U 5 NAG C 1 503 501 NAG NAG . # 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 . . . T 5 173.781 160.854 212.922 1 43.26 ? C1 NAG 502 C 1 HETATM 2 C C2 NAG . . . T 5 174.373 159.695 211.997 1 48.25 ? C2 NAG 502 C 1 HETATM 3 C C3 NAG . . . T 5 173.29 158.566 211.855 1 52.92 ? C3 NAG 502 C 1 HETATM 4 C C4 NAG . . . T 5 172.909 158.018 213.277 1 50.42 ? C4 NAG 502 C 1 HETATM 5 C C5 NAG . . . T 5 172.372 159.203 214.161 1 48.83 ? C5 NAG 502 C 1 HETATM 6 C C6 NAG . . . T 5 172.067 158.782 215.606 1 50.62 ? C6 NAG 502 C 1 HETATM 7 C C7 NAG . . . T 5 175.918 160.24 210.109 1 47.76 ? C7 NAG 502 C 1 HETATM 8 C C8 NAG . . . T 5 176.138 160.865 208.759 1 46.96 ? C8 NAG 502 C 1 HETATM 9 N N2 NAG . . . T 5 174.694 160.276 210.662 1 47.9 ? N2 NAG 502 C 1 HETATM 10 O O3 NAG . . . T 5 173.819 157.491 211.053 1 49.21 ? O3 NAG 502 C 1 HETATM 11 O O4 NAG . . . T 5 171.898 157.015 213.146 1 52.59 ? O4 NAG 502 C 1 HETATM 12 O O5 NAG . . . T 5 173.403 160.276 214.227 1 41.21 ? O5 NAG 502 C 1 HETATM 13 O O6 NAG . . . T 5 171.545 159.857 216.386 1 45.85 ? O6 NAG 502 C 1 HETATM 14 O O7 NAG . . . T 5 176.878 159.703 210.687 1 45.89 ? O7 NAG 502 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #