data_7YTP # _model_server_result.job_id H3IkBGYqf8rW7DHR62FaEw _model_server_result.datetime_utc '2024-11-12 20:40:21' _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 7ytp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":1004}' # _entry.id 7YTP # _exptl.entry_id 7YTP _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 7YTP _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YTP _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n C NAG 1 C 1 NAG C 905 NAG 2 n C NAG 2 C 2 NAG C 906 NAG 2 n D NAG 1 D 1 NAG C 907 NAG 2 n D NAG 2 D 2 NAG C 910 NAG 2 n E NAG 1 E 1 NAG C 908 NAG 2 n E NAG 2 E 2 NAG C 909 NAG 2 n F NAG 1 F 1 NAG D 905 NAG 2 n F NAG 2 F 2 NAG D 906 NAG 2 n G NAG 1 G 1 NAG D 907 NAG 2 n G NAG 2 G 2 NAG D 910 NAG 2 n H NAG 1 H 1 NAG D 908 NAG 2 n H NAG 2 H 2 NAG D 909 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 32 A CYS 36 1_555 A SG CYS 47 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 179 A CYS 183 1_555 A SG CYS 185 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 259 A CYS 263 1_555 A SG CYS 266 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 487 A CYS 491 1_555 A SG CYS 517 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 783 A CYS 787 1_555 A SG CYS 810 A CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 32 B CYS 36 1_555 B SG CYS 47 B CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 179 B CYS 183 1_555 B SG CYS 185 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 259 B CYS 263 1_555 B SG CYS 266 B CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 B SG CYS 487 B CYS 491 1_555 B SG CYS 517 B CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 783 B CYS 787 1_555 B SG CYS 810 B CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 62 A ASN 66 1_555 I C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 65 A ASN 69 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 A ND2 ASN 211 A ASN 215 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 357 A ASN 361 1_555 L C1 NAG . A NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 409 A ASN 413 1_555 K C1 NAG . A NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 A ND2 ASN 519 A ASN 523 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 A ND2 ASN 586 A ASN 590 1_555 J C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 A ND2 ASN 675 A ASN 679 1_555 M C1 NAG . A NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale9 B ND2 ASN 62 B ASN 66 1_555 O C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale10 B ND2 ASN 65 B ASN 69 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 B ND2 ASN 211 B ASN 215 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 B ND2 ASN 357 B ASN 361 1_555 R C1 NAG . B NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale13 B ND2 ASN 409 B ASN 413 1_555 Q C1 NAG . B NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 B ND2 ASN 519 B ASN 523 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale15 B ND2 ASN 586 B ASN 590 1_555 P C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale16 B ND2 ASN 675 B ASN 679 1_555 S C1 NAG . B NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale17 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale18 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale20 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale21 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale22 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _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 288 n n C1 O1 NAG sing 289 n n C1 O5 NAG sing 290 n n C1 H1 NAG sing 291 n n C2 C3 NAG sing 292 n n C2 N2 NAG sing 293 n n C2 H2 NAG sing 294 n n C3 C4 NAG sing 295 n n C3 O3 NAG sing 296 n n C3 H3 NAG sing 297 n n C4 C5 NAG sing 298 n n C4 O4 NAG sing 299 n n C4 H4 NAG sing 300 n n C5 C6 NAG sing 301 n n C5 O5 NAG sing 302 n n C5 H5 NAG sing 303 n n C6 O6 NAG sing 304 n n C6 H61 NAG sing 305 n n C6 H62 NAG sing 306 n n C7 C8 NAG sing 307 n n C7 N2 NAG sing 308 n n C7 O7 NAG doub 309 n n C8 H81 NAG sing 310 n n C8 H82 NAG sing 311 n n C8 H83 NAG sing 312 n n N2 HN2 NAG sing 313 n n O1 HO1 NAG sing 314 n n O3 HO3 NAG sing 315 n n O4 HO4 NAG sing 316 n n O6 HO6 NAG sing 317 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 7YTP _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 3 NAG A 1 1001 904 NAG NAG . J 3 NAG A 1 1002 911 NAG NAG . K 3 NAG A 1 1003 912 NAG NAG . L 3 NAG A 1 1004 913 NAG NAG . M 3 NAG A 1 1005 914 NAG NAG . N 4 JRI A 1 1006 915 JRI UNL . O 3 NAG B 1 1001 904 NAG NAG . P 3 NAG B 1 1002 911 NAG NAG . Q 3 NAG B 1 1003 912 NAG NAG . R 3 NAG B 1 1004 913 NAG NAG . S 3 NAG B 1 1005 914 NAG NAG . T 4 JRI B 1 1006 915 JRI UNL . # 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 . . . R 3 104.74 80.592 122.639 1 37.01 ? C1 NAG 1004 B 1 HETATM 2 C C2 NAG . . . R 3 103.566 80.965 123.546 1 37.01 ? C2 NAG 1004 B 1 HETATM 3 C C3 NAG . . . R 3 103.605 80.138 124.829 1 37.01 ? C3 NAG 1004 B 1 HETATM 4 C C4 NAG . . . R 3 103.675 78.652 124.503 1 37.01 ? C4 NAG 1004 B 1 HETATM 5 C C5 NAG . . . R 3 104.844 78.374 123.563 1 37.01 ? C5 NAG 1004 B 1 HETATM 6 C C6 NAG . . . R 3 104.903 76.937 123.101 1 37.01 ? C6 NAG 1004 B 1 HETATM 7 C C7 NAG . . . R 3 102.959 83.303 123.101 1 37.01 ? C7 NAG 1004 B 1 HETATM 8 C C8 NAG . . . R 3 103.073 84.722 123.57 1 37.01 ? C8 NAG 1004 B 1 HETATM 9 N N2 NAG . . . R 3 103.576 82.386 123.855 1 37.01 ? N2 NAG 1004 B 1 HETATM 10 O O3 NAG . . . R 3 102.442 80.411 125.602 1 37.01 ? O3 NAG 1004 B 1 HETATM 11 O O4 NAG . . . R 3 103.844 77.899 125.698 1 37.01 ? O4 NAG 1004 B 1 HETATM 12 O O5 NAG . . . R 3 104.723 79.182 122.384 1 37.01 ? O5 NAG 1004 B 1 HETATM 13 O O6 NAG . . . R 3 104.559 76.819 121.728 1 37.01 ? O6 NAG 1004 B 1 HETATM 14 O O7 NAG . . . R 3 102.34 83 122.086 1 37.01 ? O7 NAG 1004 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #