data_7YVB # _model_server_result.job_id WuIqKAiFmpDa-H7BFMIgIg _model_server_result.datetime_utc '2024-10-20 18:48:03' _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 7yvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":702}' # _entry.id 7YVB # _exptl.entry_id 7YVB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _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 7YVB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YVB _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 4 S N N ? 4 T N N ? 4 U N N ? 4 V N N ? 4 W N N ? 4 X N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 3 n G NAG 1 D 1 NAG D 1 NAG 3 n G NAG 2 D 2 NAG D 2 NAG 3 n H NAG 1 E 1 NAG E 1 NAG 3 n H NAG 2 E 2 NAG E 2 NAG 3 n I NAG 1 F 1 NAG F 1 NAG 3 n I NAG 2 F 2 NAG F 2 NAG 3 n J NAG 1 G 1 NAG G 1 NAG 3 n J NAG 2 G 2 NAG G 2 NAG 3 n K NAG 1 H 1 NAG H 1 NAG 3 n K NAG 2 H 2 NAG H 2 NAG 3 n L NAG 1 I 1 NAG I 1 NAG 3 n L NAG 2 I 2 NAG I 2 NAG 3 n M NAG 1 J 1 NAG J 1 NAG 3 n M NAG 2 J 2 NAG J 2 NAG 3 n N NAG 1 K 1 NAG K 1 NAG 3 n N NAG 2 K 2 NAG K 2 NAG 3 n O NAG 1 L 1 NAG L 1 NAG 3 n O NAG 2 L 2 NAG L 2 NAG 3 n P NAG 1 M 1 NAG M 1 NAG 3 n P NAG 2 M 2 NAG M 2 NAG 3 n Q NAG 1 N 1 NAG N 1 NAG 3 n Q NAG 2 N 2 NAG N 2 NAG 3 n R NAG 1 O 1 NAG O 1 NAG 3 n R NAG 2 O 2 NAG O 2 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 142 A CYS 142 1_555 A SG CYS 233 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 332 A CYS 332 1_555 A SG CYS 435 A CYS 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 350 A CYS 350 1_555 A SG CYS 431 A CYS 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 354 A CYS 354 1_555 A SG CYS 429 A CYS 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf5 A SG CYS 365 A CYS 365 1_555 A SG CYS 381 A CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 142 B CYS 142 1_555 B SG CYS 233 B CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf7 B SG CYS 332 B CYS 332 1_555 B SG CYS 435 B CYS 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 B SG CYS 350 B CYS 350 1_555 B SG CYS 431 B CYS 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 354 B CYS 354 1_555 B SG CYS 429 B CYS 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf10 B SG CYS 365 B CYS 365 1_555 B SG CYS 381 B CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 C SG CYS 142 C CYS 142 1_555 C SG CYS 233 C CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf12 C SG CYS 332 C CYS 332 1_555 C SG CYS 435 C CYS 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf13 C SG CYS 350 C CYS 350 1_555 C SG CYS 431 C CYS 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 C SG CYS 354 C CYS 354 1_555 C SG CYS 429 C CYS 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf15 C SG CYS 365 C CYS 365 1_555 C SG CYS 381 C CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 169 A ASN 169 1_555 I C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 221 A ASN 221 1_555 J C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 A ND2 ASN 331 A ASN 331 1_555 H C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 377 A ASN 377 1_555 T C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 A ND2 ASN 393 A ASN 393 1_555 G C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 A ND2 ASN 401 A ASN 401 1_555 S C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B ND2 ASN 169 B ASN 169 1_555 M C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale8 B ND2 ASN 221 B ASN 221 1_555 N C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale9 B ND2 ASN 331 B ASN 331 1_555 L C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 B ND2 ASN 377 B ASN 377 1_555 U C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 B ND2 ASN 393 B ASN 393 1_555 K C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale12 B ND2 ASN 401 B ASN 401 1_555 V C1 NAG . B NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 C ND2 ASN 169 C ASN 169 1_555 Q C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale14 C ND2 ASN 221 C ASN 221 1_555 R C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale15 C ND2 ASN 331 C ASN 331 1_555 P C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 C ND2 ASN 377 C ASN 377 1_555 W C1 NAG . C NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale17 C ND2 ASN 393 C ASN 393 1_555 O C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale18 C ND2 ASN 401 C ASN 401 1_555 X C1 NAG . C NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 D C ARG 3 P ARG 3 1_555 D N NFA 4 P NFA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale20 E C ARG 3 Q ARG 3 1_555 E N NFA 4 Q NFA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale21 F C ARG 3 R ARG 3 1_555 F N NFA 4 R NFA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale22 G O4 NAG . D NAG 1 1_555 G C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale23 H O4 NAG . E NAG 1 1_555 H C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale24 I O4 NAG . F NAG 1 1_555 I C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale25 J O4 NAG . G NAG 1 1_555 J C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale26 K O4 NAG . H NAG 1 1_555 K C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale27 L O4 NAG . I NAG 1 1_555 L C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale28 M O4 NAG . J NAG 1 1_555 M C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale29 N O4 NAG . K NAG 1 1_555 N C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale30 O O4 NAG . L NAG 1 1_555 O C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale31 P O4 NAG . M NAG 1 1_555 P C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale32 Q O4 NAG . N NAG 1 1_555 Q C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale33 R O4 NAG . O NAG 1 1_555 R C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _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 7YVB _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 S 4 NAG A 1 701 701 NAG NAG . T 4 NAG A 1 702 702 NAG NAG . U 4 NAG B 1 701 701 NAG NAG . V 4 NAG B 1 702 702 NAG NAG . W 4 NAG C 1 701 701 NAG NAG . X 4 NAG C 1 702 702 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 4 105.992 100.508 153.995 1 98.1 ? C1 NAG 702 A 1 HETATM 2 C C2 NAG . . . T 4 105.35 100.047 152.684 1 98.1 ? C2 NAG 702 A 1 HETATM 3 C C3 NAG . . . T 4 103.832 100.206 152.748 1 98.1 ? C3 NAG 702 A 1 HETATM 4 C C4 NAG . . . T 4 103.272 99.526 153.989 1 98.1 ? C4 NAG 702 A 1 HETATM 5 C C5 NAG . . . T 4 103.995 100.032 155.231 1 98.1 ? C5 NAG 702 A 1 HETATM 6 C C6 NAG . . . T 4 103.558 99.333 156.497 1 98.1 ? C6 NAG 702 A 1 HETATM 7 C C7 NAG . . . T 4 105.839 100.345 150.295 1 98.1 ? C7 NAG 702 A 1 HETATM 8 C C8 NAG . . . T 4 106.451 101.239 149.26 1 98.1 ? C8 NAG 702 A 1 HETATM 9 N N2 NAG . . . T 4 105.893 100.786 151.556 1 98.1 ? N2 NAG 702 A 1 HETATM 10 O O3 NAG . . . T 4 103.245 99.635 151.584 1 98.1 ? O3 NAG 702 A 1 HETATM 11 O O4 NAG . . . T 4 101.882 99.8 154.111 1 98.1 ? O4 NAG 702 A 1 HETATM 12 O O5 NAG . . . T 4 105.404 99.803 155.093 1 98.1 ? O5 NAG 702 A 1 HETATM 13 O O6 NAG . . . T 4 102.416 99.959 157.063 1 98.1 ? O6 NAG 702 A 1 HETATM 14 O O7 NAG . . . T 4 105.318 99.273 150.004 1 98.1 ? O7 NAG 702 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 392 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 14 #