data_7VFV # _model_server_result.job_id CZdlpwfNQZD3MMPWnzmxeg _model_server_result.datetime_utc '2024-12-22 06:15:36' _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 7vfv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"IA","auth_seq_id":1207}' # _entry.id 7VFV # _exptl.entry_id 7VFV _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 11 _entity.src_method syn _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 7VFV _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VFV _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 _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 ? 11 DA N N ? 11 EA N N ? 11 FA N N ? 11 GA N N ? 11 HA N N ? 11 IA N N ? 11 JA N N ? 11 KA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 5 3 2 BMA NAG C1 O1 . O3 HO3 . 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 C 1 NAG B 1235 NAG 4 n D NAG 2 C 2 NAG B 1236 NAG 4 n D BMA 3 C 3 BMA B 1237 BMA 4 n E NAG 1 E 1 NAG B 1241 NAG 4 n E NAG 2 E 2 NAG B 1242 NAG 4 n E BMA 3 E 3 BMA B 1243 BMA 5 n F NAG 1 F 1 NAG B 1247 NAG 5 n F NAG 2 F 2 NAG B 1248 NAG 5 n F BMA 3 F 3 BMA B 1249 BMA # 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 253 A CYS 253 1_555 A SG CYS 277 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 268 A CYS 268 1_555 A SG CYS 283 A CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 1311 A CYS 1311 1_555 A SG CYS 1322 A CYS 1322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 A SG CYS 1670 A CYS 1670 1_555 A SG CYS 1679 A CYS 1679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 B SG CYS 303 B CYS 303 1_555 B SG CYS 1044 B CYS 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 B SG CYS 354 B CYS 354 1_555 B SG CYS 1059 B CYS 1059 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 B SG CYS 404 B CYS 404 1_555 B SG CYS 1071 B CYS 1071 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 B SG CYS 667 B CYS 667 1_555 B SG CYS 697 B CYS 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 B SG CYS 904 B CYS 904 1_555 B SG CYS 974 B CYS 974 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf10 B SG CYS 996 B CYS 996 1_555 B SG CYS 1026 B CYS 1026 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 B SG CYS 999 B CYS 999 1_555 B SG CYS 1024 B CYS 1024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A OH TYR 1289 A TYR 1289 1_555 AA C32 6IX . A 6IX 2421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale2 B ND2 ASN 92 B ASN 92 1_555 DA C1 NAG . B NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 B ND2 ASN 184 B ASN 184 1_555 KA C1 NAG . B NAG 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 B ND2 ASN 324 B ASN 324 1_555 EA C1 NAG . B NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 348 B ASN 348 1_555 FA C1 NAG . B NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 B ND2 ASN 468 B ASN 468 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B ND2 ASN 604 B ASN 604 1_555 GA C1 NAG . B NAG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 B ND2 ASN 613 B ASN 613 1_555 HA C1 NAG . B NAG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale9 B ND2 ASN 675 B ASN 675 1_555 IA C1 NAG . B NAG 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale10 B ND2 ASN 824 B ASN 824 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 B ND2 ASN 888 B ASN 888 1_555 JA C1 NAG . B NAG 1208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 B ND2 ASN 895 B ASN 895 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale13 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale14 D O4 NAG . C NAG 2 1_555 D C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale15 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale16 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale18 F O3 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc1 A OD2 ASP 122 A ASP 122 1_555 CA CA CA . B CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc2 A OE2 GLU 314 A GLU 314 1_555 BA CA CA . A CA 2422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc3 A OE1 GLU 663 A GLU 663 1_555 BA CA CA . A CA 2422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc4 A OE1 GLU 1365 A GLU 1365 1_555 BA CA CA . A CA 2422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc5 A OE2 GLU 1365 A GLU 1365 1_555 BA CA CA . A CA 2422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc6 B OG SER 263 B SER 263 1_555 CA CA CA . B CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc7 B OG1 THR 331 B THR 331 1_555 CA CA CA . B CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? # _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_ _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 7VFV _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 G 6 R16 A 1 2401 2402 R16 R16 . H 6 R16 A 1 2402 2403 R16 R16 . I 6 R16 A 1 2403 2404 R16 R16 . J 7 Y01 A 1 2404 2405 Y01 Y01 . K 6 R16 A 1 2405 2408 R16 R16 . L 6 R16 A 1 2406 2409 R16 R16 . M 6 R16 A 1 2407 2410 R16 R16 . N 6 R16 A 1 2408 2411 R16 R16 . O 6 R16 A 1 2409 2413 R16 R16 . P 7 Y01 A 1 2410 2414 Y01 Y01 . Q 6 R16 A 1 2411 2415 R16 R16 . R 6 R16 A 1 2412 2416 R16 R16 . S 6 R16 A 1 2413 2417 R16 R16 . T 6 R16 A 1 2414 2419 R16 R16 . U 6 R16 A 1 2415 2421 R16 R16 . V 6 R16 A 1 2416 2422 R16 R16 . W 6 R16 A 1 2417 2423 R16 R16 . X 6 R16 A 1 2418 2424 R16 R16 . Y 7 Y01 A 1 2419 2426 Y01 Y01 . Z 8 PT5 A 1 2420 2427 PT5 PT5 . AA 9 6IX A 1 2421 2428 6IX LIG . BA 10 CA A 1 2422 1 CA CA . CA 10 CA B 1 1201 1201 CA CA . DA 11 NAG B 1 1202 1238 NAG NAG . EA 11 NAG B 1 1203 1239 NAG NAG . FA 11 NAG B 1 1204 1240 NAG NAG . GA 11 NAG B 1 1205 1244 NAG NAG . HA 11 NAG B 1 1206 1245 NAG NAG . IA 11 NAG B 1 1207 1246 NAG NAG . JA 11 NAG B 1 1208 1250 NAG NAG . KA 11 NAG B 1 1209 1251 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 . . . IA 11 135.312 169.403 235.158 1 136.34 ? C1 NAG 1207 B 1 HETATM 2 C C2 NAG . . . IA 11 135.032 170.61 234.267 1 136.34 ? C2 NAG 1207 B 1 HETATM 3 C C3 NAG . . . IA 11 133.961 171.493 234.899 1 136.34 ? C3 NAG 1207 B 1 HETATM 4 C C4 NAG . . . IA 11 132.721 170.674 235.232 1 136.34 ? C4 NAG 1207 B 1 HETATM 5 C C5 NAG . . . IA 11 133.097 169.453 236.068 1 136.34 ? C5 NAG 1207 B 1 HETATM 6 C C6 NAG . . . IA 11 131.93 168.526 236.315 1 136.34 ? C6 NAG 1207 B 1 HETATM 7 C C7 NAG . . . IA 11 137.018 171.201 232.948 1 136.34 ? C7 NAG 1207 B 1 HETATM 8 C C8 NAG . . . IA 11 138.23 172.077 232.861 1 136.34 ? C8 NAG 1207 B 1 HETATM 9 N N2 NAG . . . IA 11 136.246 171.374 234.026 1 136.34 ? N2 NAG 1207 B 1 HETATM 10 O O3 NAG . . . IA 11 133.622 172.541 233.998 1 136.34 ? O3 NAG 1207 B 1 HETATM 11 O O4 NAG . . . IA 11 131.796 171.471 235.963 1 136.34 ? O4 NAG 1207 B 1 HETATM 12 O O5 NAG . . . IA 11 134.099 168.684 235.388 1 136.34 ? O5 NAG 1207 B 1 HETATM 13 O O6 NAG . . . IA 11 131.338 168.098 235.097 1 136.34 ? O6 NAG 1207 B 1 HETATM 14 O O7 NAG . . . IA 11 136.75 170.373 232.083 1 136.34 ? O7 NAG 1207 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #