data_8E56 # _model_server_result.job_id udpserUpjSLu6_V4EfOqaA _model_server_result.datetime_utc '2024-11-04 23:09:54' _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 8e56 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":1204}' # _entry.id 8E56 # _exptl.entry_id 8E56 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 7 _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 8E56 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E56 _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 _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 ? 10 O N N ? 10 P N N ? 10 Q N N ? 10 R N N ? 10 S N N ? 10 T N N ? 10 U N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . 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 B 1 NAG F 1101 NAG 4 n D NAG 2 B 2 NAG F 1102 NAG 4 n E NAG 1 C 1 NAG F 1103 NAG 4 n E NAG 2 C 2 NAG F 1104 NAG 4 n F NAG 1 D 1 NAG F 1105 NAG 4 n F NAG 2 D 2 NAG F 1106 NAG 4 n G NAG 1 G 1 NAG F 1107 NAG 4 n G NAG 2 G 2 NAG F 1108 NAG 5 n H NAG 1 H 1 NAG F 1109 NAG 5 n H NAG 2 H 2 NAG F 1110 NAG 5 n H NAG 3 H 3 NAG F 1111 NAG 6 n I NAG 1 I 1 NAG F 1119 NAG 6 n I NAG 2 I 2 NAG F 1120 NAG 6 n I BMA 3 I 3 BMA F 1121 BMA 6 n J NAG 1 J 1 NAG F 1122 NAG 6 n J NAG 2 J 2 NAG F 1123 NAG 6 n J BMA 3 J 3 BMA F 1124 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 226 A CYS 226 1_555 A SG CYS 254 A CYS 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 245 A CYS 245 1_555 A SG CYS 261 A CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 957 A CYS 957 1_555 A SG CYS 968 A CYS 968 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 1338 A CYS 1338 1_555 A SG CYS 1352 A CYS 1352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 57 E CYS 57 1_555 B SG CYS 80 E CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 C SG CYS 305 F CYS 305 1_555 C SG CYS 1047 F CYS 1047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 C SG CYS 356 F CYS 356 1_555 C SG CYS 1062 F CYS 1062 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 C SG CYS 406 F CYS 406 1_555 C SG CYS 1074 F CYS 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 670 F CYS 670 1_555 C SG CYS 700 F CYS 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 844 F CYS 844 1_555 C SG CYS 853 F CYS 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 C SG CYS 907 F CYS 907 1_555 C SG CYS 977 F CYS 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf12 C SG CYS 999 F CYS 999 1_555 C SG CYS 1029 F CYS 1029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 C SG CYS 1002 F CYS 1002 1_555 C SG CYS 1027 F CYS 1027 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 C ND2 ASN 94 F ASN 92 1_555 Q C1 NAG . F NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale2 C ND2 ASN 186 F ASN 186 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 C ND2 ASN 326 F ASN 326 1_555 O C1 NAG . F NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 C ND2 ASN 350 F ASN 350 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale5 C ND2 ASN 470 F ASN 470 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 C ND2 ASN 606 F ASN 606 1_555 R C1 NAG . F NAG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 C ND2 ASN 615 F ASN 615 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 C ND2 ASN 784 F ASN 784 1_555 S C1 NAG . F NAG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale9 C ND2 ASN 827 F ASN 827 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale10 C ND2 ASN 891 F ASN 891 1_555 P C1 NAG . F NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale11 C ND2 ASN 898 F ASN 898 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale12 C ND2 ASN 988 F ASN 988 1_555 U C1 NAG . F NAG 1208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale13 C ND2 ASN 1001 F ASN 1001 1_555 T C1 NAG . F NAG 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale14 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale15 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale17 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 H O4 NAG . H NAG 2 1_555 H C1 NAG . H NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale20 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale21 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale22 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale23 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 A OD2 ASP 78 A ASP 78 1_555 N CA CA . F CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.055 ? metalc ? metalc2 A OE1 GLU 292 A GLU 292 1_555 K CA CA . A CA 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc3 A OE1 GLU 614 A GLU 614 1_555 K CA CA . A CA 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc4 A OE2 GLU 1014 A GLU 1014 1_555 K CA CA . A CA 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc5 A O GLY 1322 A GLY 1322 1_555 K CA CA . A CA 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.111 ? metalc ? metalc6 C OG SER 263 F SER 263 1_555 N CA CA . F CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc7 C OG SER 265 F SER 265 1_555 N CA CA . F CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc8 C OG1 THR 333 F THR 333 1_555 N CA CA . F CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? # _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 453 n n C1 O1 NAG sing 454 n n C1 O5 NAG sing 455 n n C1 H1 NAG sing 456 n n C2 C3 NAG sing 457 n n C2 N2 NAG sing 458 n n C2 H2 NAG sing 459 n n C3 C4 NAG sing 460 n n C3 O3 NAG sing 461 n n C3 H3 NAG sing 462 n n C4 C5 NAG sing 463 n n C4 O4 NAG sing 464 n n C4 H4 NAG sing 465 n n C5 C6 NAG sing 466 n n C5 O5 NAG sing 467 n n C5 H5 NAG sing 468 n n C6 O6 NAG sing 469 n n C6 H61 NAG sing 470 n n C6 H62 NAG sing 471 n n C7 C8 NAG sing 472 n n C7 N2 NAG sing 473 n n C7 O7 NAG doub 474 n n C8 H81 NAG sing 475 n n C8 H82 NAG sing 476 n n C8 H83 NAG sing 477 n n N2 HN2 NAG sing 478 n n O1 HO1 NAG sing 479 n n O3 HO3 NAG sing 480 n n O4 HO4 NAG sing 481 n n O6 HO6 NAG sing 482 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 8E56 _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 K 7 CA A 1 1901 1902 CA CA . L 8 BBI A 1 1902 2001 BBI IAK . M 9 3PE A 1 1903 2101 3PE 3PE . N 7 CA F 1 1201 1903 CA CA . O 10 NAG F 1 1202 1112 NAG NAG . P 10 NAG F 1 1203 1113 NAG NAG . Q 10 NAG F 1 1204 1114 NAG NAG . R 10 NAG F 1 1205 1115 NAG NAG . S 10 NAG F 1 1206 1116 NAG NAG . T 10 NAG F 1 1207 1117 NAG NAG . U 10 NAG F 1 1208 1118 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 . . . Q 10 184.09 141.937 225.959 1 91.63 ? C1 NAG 1204 F 1 HETATM 2 C C2 NAG . . . Q 10 185.55 141.517 225.71 1 91.87 ? C2 NAG 1204 F 1 HETATM 3 C C3 NAG . . . Q 10 186.39 141.736 226.964 1 92.64 ? C3 NAG 1204 F 1 HETATM 4 C C4 NAG . . . Q 10 186.255 143.175 227.443 1 94.3 ? C4 NAG 1204 F 1 HETATM 5 C C5 NAG . . . Q 10 184.783 143.527 227.645 1 91.89 ? C5 NAG 1204 F 1 HETATM 6 C C6 NAG . . . Q 10 184.571 144.975 228.015 1 90.79 ? C6 NAG 1204 F 1 HETATM 7 C C7 NAG . . . Q 10 186.514 139.716 224.347 1 91.01 ? C7 NAG 1204 F 1 HETATM 8 C C8 NAG . . . Q 10 186.458 138.259 223.998 1 88.72 ? C8 NAG 1204 F 1 HETATM 9 N N2 NAG . . . Q 10 185.636 140.136 225.263 1 88.44 ? N2 NAG 1204 F 1 HETATM 10 O O3 NAG . . . Q 10 187.753 141.444 226.681 1 91.73 ? O3 NAG 1204 F 1 HETATM 11 O O4 NAG . . . Q 10 186.957 143.355 228.667 1 95.23 ? O4 NAG 1204 F 1 HETATM 12 O O5 NAG . . . Q 10 184.053 143.301 226.429 1 94.82 ? O5 NAG 1204 F 1 HETATM 13 O O6 NAG . . . Q 10 184.934 145.839 226.947 1 91.3 ? O6 NAG 1204 F 1 HETATM 14 O O7 NAG . . . Q 10 187.317 140.48 223.819 1 91.42 ? O7 NAG 1204 F 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #