data_3JD8 # _model_server_result.job_id 7ieJmV6Cl8LKdMuThIuMng _model_server_result.datetime_utc '2024-11-16 05:47:31' _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 3jd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":1323}' # _entry.id 3JD8 # _exptl.entry_id 3JD8 _exptl.method 'ELECTRON MICROSCOPY' # _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 11 _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 3JD8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JD8 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 G N N ? 5 H N N ? 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 # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 4 4 3 MAN BMA 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 2 n B NAG 1 B 1 NAG A 1301 NAG 2 n B NAG 2 B 2 NAG A 1302 NAG 2 n C NAG 1 C 1 NAG A 1304 NAG 2 n C NAG 2 C 2 NAG A 1305 NAG 3 n D NAG 1 D 1 NAG A 1306 NAG 3 n D NAG 2 D 2 NAG A 1307 NAG 3 n D BMA 3 D 3 BMA A 1308 BMA 2 n E NAG 1 E 1 NAG A 1310 NAG 2 n E NAG 2 E 2 NAG A 1311 NAG 4 n F NAG 1 F 1 NAG A 1312 NAG 4 n F NAG 2 F 2 NAG A 1313 NAG 4 n F BMA 3 F 3 BMA A 1314 BMA 4 n F MAN 4 F 4 MAN A 1315 MAN # 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 25 A CYS 25 1_555 A SG CYS 74 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 31 A CYS 31 1_555 A SG CYS 42 A CYS 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf3 A SG CYS 63 A CYS 63 1_555 A SG CYS 109 A CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf4 A SG CYS 75 A CYS 75 1_555 A SG CYS 113 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf5 A SG CYS 97 A CYS 97 1_555 A SG CYS 238 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 100 A CYS 100 1_555 A SG CYS 160 A CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 A SG CYS 177 A CYS 177 1_555 A SG CYS 184 A CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf8 A SG CYS 227 A CYS 227 1_555 A SG CYS 243 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? disulf ? disulf9 A SG CYS 468 A CYS 468 1_555 A SG CYS 479 A CYS 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf10 A SG CYS 516 A CYS 516 1_555 A SG CYS 533 A CYS 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? covale ? covale1 A ND2 ASN 122 A ASN 122 1_555 I C1 NAG . A NAG 1316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale2 A ND2 ASN 222 A ASN 222 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 1064 A ASN 1064 1_555 M C1 NAG . A NAG 1320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale9 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale10 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale11 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? # _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 360 n n C1 O1 NAG sing 361 n n C1 O5 NAG sing 362 n n C1 H1 NAG sing 363 n n C2 C3 NAG sing 364 n n C2 N2 NAG sing 365 n n C2 H2 NAG sing 366 n n C3 C4 NAG sing 367 n n C3 O3 NAG sing 368 n n C3 H3 NAG sing 369 n n C4 C5 NAG sing 370 n n C4 O4 NAG sing 371 n n C4 H4 NAG sing 372 n n C5 C6 NAG sing 373 n n C5 O5 NAG sing 374 n n C5 H5 NAG sing 375 n n C6 O6 NAG sing 376 n n C6 H61 NAG sing 377 n n C6 H62 NAG sing 378 n n C7 C8 NAG sing 379 n n C7 N2 NAG sing 380 n n C7 O7 NAG doub 381 n n C8 H81 NAG sing 382 n n C8 H82 NAG sing 383 n n C8 H83 NAG sing 384 n n N2 HN2 NAG sing 385 n n O1 HO1 NAG sing 386 n n O3 HO3 NAG sing 387 n n O4 HO4 NAG sing 388 n n O6 HO6 NAG sing 389 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 3JD8 _atom_sites.fract_transf_matrix[1][1] 0.003827 _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] 0.003827 _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] 0.003827 _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 G 5 NAG A 1 1303 1303 NAG NAG . H 5 NAG A 1 1309 1309 NAG NAG . I 5 NAG A 1 1316 1316 NAG NAG . J 5 NAG A 1 1317 1317 NAG NAG . K 5 NAG A 1 1318 1318 NAG NAG . L 5 NAG A 1 1319 1319 NAG NAG . M 5 NAG A 1 1320 1320 NAG NAG . N 5 NAG A 1 1321 1321 NAG NAG . O 5 NAG A 1 1322 1322 NAG NAG . P 5 NAG A 1 1323 1323 NAG NAG . Q 5 NAG A 1 1324 1324 NAG NAG . R 6 CLR A 1 1325 1325 CLR CLR . # 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 . . . P 5 118.253 102.69 173.845 1 338.66 ? C1 NAG 1323 A 1 HETATM 2 C C2 NAG . . . P 5 116.761 102.518 174.101 1 338.66 ? C2 NAG 1323 A 1 HETATM 3 C C3 NAG . . . P 5 116.496 101.312 174.995 1 338.66 ? C3 NAG 1323 A 1 HETATM 4 C C4 NAG . . . P 5 117.235 100.081 174.486 1 338.66 ? C4 NAG 1323 A 1 HETATM 5 C C5 NAG . . . P 5 118.699 100.399 174.206 1 338.66 ? C5 NAG 1323 A 1 HETATM 6 C C6 NAG . . . P 5 119.419 99.189 173.625 1 338.66 ? C6 NAG 1323 A 1 HETATM 7 C C7 NAG . . . P 5 115.738 104.714 173.976 1 338.66 ? C7 NAG 1323 A 1 HETATM 8 C C8 NAG . . . P 5 114.856 104.31 172.832 1 338.66 ? C8 NAG 1323 A 1 HETATM 9 N N2 NAG . . . P 5 116.221 103.717 174.712 1 338.66 ? N2 NAG 1323 A 1 HETATM 10 O O3 NAG . . . P 5 115.089 101.044 175.03 1 338.66 ? O3 NAG 1323 A 1 HETATM 11 O O4 NAG . . . P 5 117.151 99.036 175.462 1 338.66 ? O4 NAG 1323 A 1 HETATM 12 O O5 NAG . . . P 5 118.782 101.488 173.289 1 338.66 ? O5 NAG 1323 A 1 HETATM 13 O O6 NAG . . . P 5 120.026 98.439 174.684 1 338.66 ? O6 NAG 1323 A 1 HETATM 14 O O7 NAG . . . P 5 115.995 105.882 174.217 1 338.66 ? O7 NAG 1323 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 828 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #