data_8TP2 # _model_server_result.job_id iyEkm0zjmrzev-PjqcbEWQ _model_server_result.datetime_utc '2024-10-25 20:21:31' _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 8tp2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":504}' # _entry.id 8TP2 # _exptl.entry_id 8TP2 _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 10 _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 8TP2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TP2 _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 I N N ? 5 J N N ? 5 K N N ? 5 L N N ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 1 FUC NAG C1 O1 . O6 HO6 . 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 F NAG 1 D 1 NAG C 498 NAG 4 n F NAG 2 D 2 NAG C 499 NAG 4 n F FUC 3 D 3 FUC C 500 FUC 4 n G NAG 1 E 1 NAG A 498 NAG 4 n G NAG 2 E 2 NAG A 499 NAG 4 n G FUC 3 E 3 FUC A 500 FUC 4 n H NAG 1 F 1 NAG B 498 NAG 4 n H NAG 2 F 2 NAG B 499 NAG 4 n H FUC 3 F 3 FUC B 500 FUC # 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 22 H CYS 22 1_555 A SG CYS 95 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 C SG CYS 19 C CYS 14 1_555 C SG CYS 477 C CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 C SG CYS 57 C CYS 52 1_555 C SG CYS 288 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 C SG CYS 70 C CYS 64 1_555 C SG CYS 82 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 C SG CYS 105 C CYS 97 1_555 C SG CYS 149 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf7 C SG CYS 292 C CYS 281 1_555 C SG CYS 316 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 C SG CYS 484 C CYS 473 1_555 C SG CYS 488 C CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf9 D SG CYS 19 A CYS 14 1_555 D SG CYS 477 A CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 D SG CYS 57 A CYS 52 1_555 D SG CYS 288 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 D SG CYS 70 A CYS 64 1_555 D SG CYS 82 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 D SG CYS 105 A CYS 97 1_555 D SG CYS 149 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf13 D SG CYS 292 A CYS 281 1_555 D SG CYS 316 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf14 D SG CYS 484 A CYS 473 1_555 D SG CYS 488 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf15 E SG CYS 19 B CYS 14 1_555 E SG CYS 477 B CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf16 E SG CYS 57 B CYS 52 1_555 E SG CYS 288 B CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf17 E SG CYS 70 B CYS 64 1_555 E SG CYS 82 B CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf18 E SG CYS 105 B CYS 97 1_555 E SG CYS 149 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf19 E SG CYS 292 B CYS 281 1_555 E SG CYS 316 B CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf20 E SG CYS 484 B CYS 473 1_555 E SG CYS 488 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? covale ? covale1 C ND2 ASN 26 C ASN 21 1_555 L C1 NAG . C NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale2 C ND2 ASN 38 C ASN 33 1_555 I C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.516 ? covale ? covale3 C ND2 ASN 179 C ASN 169 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.51 ? covale ? covale4 C ND2 ASN 300 C ASN 289 1_555 J C1 NAG . C NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? covale ? covale5 C ND2 ASN 494 C ASN 483 1_555 K C1 NAG . C NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 D ND2 ASN 26 A ASN 21 1_555 M C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.519 ? covale ? covale7 D ND2 ASN 38 A ASN 33 1_555 N C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? covale ? covale8 D ND2 ASN 179 A ASN 169 1_555 G C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? covale ? covale9 D ND2 ASN 300 A ASN 289 1_555 O C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.524 ? covale ? covale10 E ND2 ASN 26 B ASN 21 1_555 P C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale11 E ND2 ASN 38 B ASN 33 1_555 Q C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale12 E ND2 ASN 179 B ASN 169 1_555 H C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? covale ? covale13 E ND2 ASN 300 B ASN 289 1_555 R C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.526 ? covale ? covale14 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.504 ? covale ? covale15 F O6 NAG . D NAG 1 1_555 F C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale16 G O4 NAG . E NAG 1 1_555 G C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.517 ? covale ? covale17 G O6 NAG . E NAG 1 1_555 G C1 FUC . E FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? covale ? covale18 H O4 NAG . F NAG 1 1_555 H C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.503 ? covale ? covale19 H O6 NAG . F NAG 1 1_555 H C1 FUC . F FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.496 ? # _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 258 n n C1 O1 NAG sing 259 n n C1 O5 NAG sing 260 n n C1 H1 NAG sing 261 n n C2 C3 NAG sing 262 n n C2 N2 NAG sing 263 n n C2 H2 NAG sing 264 n n C3 C4 NAG sing 265 n n C3 O3 NAG sing 266 n n C3 H3 NAG sing 267 n n C4 C5 NAG sing 268 n n C4 O4 NAG sing 269 n n C4 H4 NAG sing 270 n n C5 C6 NAG sing 271 n n C5 O5 NAG sing 272 n n C5 H5 NAG sing 273 n n C6 O6 NAG sing 274 n n C6 H61 NAG sing 275 n n C6 H62 NAG sing 276 n n C7 C8 NAG sing 277 n n C7 N2 NAG sing 278 n n C7 O7 NAG doub 279 n n C8 H81 NAG sing 280 n n C8 H82 NAG sing 281 n n C8 H83 NAG sing 282 n n N2 HN2 NAG sing 283 n n O1 HO1 NAG sing 284 n n O3 HO3 NAG sing 285 n n O4 HO4 NAG sing 286 n n O6 HO6 NAG sing 287 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 8TP2 _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 5 NAG C 1 501 497 NAG NAG . J 5 NAG C 1 502 501 NAG NAG . K 5 NAG C 1 503 502 NAG NAG . L 5 NAG C 1 504 503 NAG NAG . M 5 NAG A 1 501 496 NAG NAG . N 5 NAG A 1 502 497 NAG NAG . O 5 NAG A 1 503 501 NAG NAG . P 5 NAG B 1 501 496 NAG NAG . Q 5 NAG B 1 502 497 NAG NAG . R 5 NAG B 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 . . . L 5 209.097 164.225 126.019 1 30 ? C1 NAG 504 C 1 HETATM 2 C C2 NAG . . . L 5 209.934 163.015 126.442 1 30 ? C2 NAG 504 C 1 HETATM 3 C C3 NAG . . . L 5 211.207 163.462 127.167 1 30 ? C3 NAG 504 C 1 HETATM 4 C C4 NAG . . . L 5 211.942 164.543 126.38 1 30 ? C4 NAG 504 C 1 HETATM 5 C C5 NAG . . . L 5 210.961 165.648 126.023 1 30 ? C5 NAG 504 C 1 HETATM 6 C C6 NAG . . . L 5 211.638 166.773 125.261 1 30 ? C6 NAG 504 C 1 HETATM 7 C C7 NAG . . . L 5 208.277 161.246 126.838 1 30 ? C7 NAG 504 C 1 HETATM 8 C C8 NAG . . . L 5 207.457 160.523 127.868 1 30 ? C8 NAG 504 C 1 HETATM 9 N N2 NAG . . . L 5 209.169 162.128 127.302 1 30 ? N2 NAG 504 C 1 HETATM 10 O O3 NAG . . . L 5 212.039 162.316 127.389 1 30 ? O3 NAG 504 C 1 HETATM 11 O O4 NAG . . . L 5 212.945 165.19 127.174 1 30 ? O4 NAG 504 C 1 HETATM 12 O O5 NAG . . . L 5 209.893 165.114 125.252 1 30 ? O5 NAG 504 C 1 HETATM 13 O O6 NAG . . . L 5 211.261 166.653 123.897 1 30 ? O6 NAG 504 C 1 HETATM 14 O O7 NAG . . . L 5 208.129 161.03 125.642 1 30 ? O7 NAG 504 C 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #