data_8XVM # _model_server_result.job_id 9N_5xaMwTcjaS1BVC87O6A _model_server_result.datetime_utc '2024-12-22 07:26:31' _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 8xvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":1311}' # _entry.id 8XVM # _exptl.entry_id 8XVM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 15 _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 8XVM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XVM _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 1 2 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 1 3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? -0.5 0.866 0 -0.866 -0.5 0 0 0 1 122.3313 456.5481 0 3 'point symmetry operation' ? ? -0.5 -0.866 0 0.866 -0.5 0 0 0 1 456.5485 122.3327 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K N N ? 6 L N N ? 6 M N N ? 6 N N N ? 6 O N N ? 6 P N N ? 6 Q N N ? 6 R N N ? 6 S N N ? 6 T N N ? 6 U N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 5 5 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 3 n C NAG 1 E 1 NAG E 1 NAG 3 n C NAG 2 E 2 NAG E 2 NAG 3 n D NAG 1 F 1 NAG F 1 NAG 3 n D NAG 2 F 2 NAG F 2 NAG 4 n E NAG 1 M 1 NAG M 1 NAG 4 n E NAG 2 M 2 NAG M 2 NAG 4 n E BMA 3 M 3 BMA M 3 BMA 5 n F NAG 1 N 1 NAG N 1 NAG 5 n F NAG 2 N 2 NAG N 2 NAG 5 n F BMA 3 N 3 BMA N 3 BMA 5 n F MAN 4 N 4 MAN N 4 MAN 5 n F MAN 5 N 5 MAN N 5 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 119 A CYS 131 1_555 A SG CYS 153 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 277 A CYS 290 1_555 A SG CYS 287 A CYS 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 322 A CYS 335 1_555 A SG CYS 347 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 365 A CYS 378 1_555 A SG CYS 418 A CYS 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 377 A CYS 390 1_555 A SG CYS 510 A CYS 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 466 A CYS 479 1_555 A SG CYS 473 A CYS 486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 523 A CYS 536 1_555 A SG CYS 575 A CYS 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 A SG CYS 602 A CYS 615 1_555 A SG CYS 634 A CYS 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 A SG CYS 647 A CYS 660 1_555 A SG CYS 656 A CYS 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 A SG CYS 723 A CYS 736 1_555 A SG CYS 745 A CYS 758 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 A SG CYS 728 A CYS 741 1_555 A SG CYS 734 A CYS 747 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf12 A SG CYS 1017 A CYS 1030 1_555 A SG CYS 1028 A CYS 1041 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 A SG CYS 1067 A CYS 1080 1_555 A SG CYS 1111 A CYS 1124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 B SG CYS 115 D CYS 133 1_555 B SG CYS 123 D CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 B SG CYS 326 D CYS 344 1_555 B SG CYS 343 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf16 B SG CYS 512 D CYS 530 1_555 B SG CYS 524 D CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 51 A ASN 61 1_555 G C1 NAG . A NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 110 A ASN 122 1_555 H C1 NAG . A NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A ND2 ASN 152 A ASN 165 1_555 I C1 NAG . A NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 220 A ASN 233 1_555 J C1 NAG . A NAG 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 A ND2 ASN 268 A ASN 281 1_555 K C1 NAG . A NAG 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 A ND2 ASN 317 A ASN 330 1_555 R C1 NAG . A NAG 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 A ND2 ASN 601 A ASN 614 1_555 L C1 NAG . A NAG 1306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale8 A ND2 ASN 642 A ASN 655 1_555 M C1 NAG . A NAG 1307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 A ND2 ASN 694 A ASN 707 1_555 N C1 NAG . A NAG 1308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 A ND2 ASN 702 A ASN 715 1_555 C C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 A ND2 ASN 786 A ASN 799 1_555 D C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 A ND2 ASN 1059 A ASN 1072 1_555 O C1 NAG . A NAG 1309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale13 A ND2 ASN 1083 A ASN 1096 1_555 P C1 NAG . A NAG 1310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 A ND2 ASN 1119 A ASN 1132 1_555 Q C1 NAG . A NAG 1311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale15 B ND2 ASN 35 D ASN 53 1_555 U C1 NAG . D NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale16 B ND2 ASN 72 D ASN 90 1_555 E C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale17 B ND2 ASN 85 D ASN 103 1_555 F C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale18 B ND2 ASN 304 D ASN 322 1_555 S C1 NAG . D NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale19 B ND2 ASN 414 D ASN 432 1_555 T C1 NAG . D NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale20 C O4 NAG . E NAG 1 1_555 C C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale21 D O4 NAG . F NAG 1 1_555 D C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale22 E O4 NAG . M NAG 1 1_555 E C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale23 E O4 NAG . M NAG 2 1_555 E C1 BMA . M BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale24 F O4 NAG . N NAG 1 1_555 F C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale25 F O4 NAG . N NAG 2 1_555 F C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale26 F O3 BMA . N BMA 3 1_555 F C1 MAN . N MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale27 F O6 BMA . N BMA 3 1_555 F C1 MAN . N MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 8XVM _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 NAG A 1 1301 1299 NAG NAG . H 6 NAG A 1 1302 1300 NAG NAG . I 6 NAG A 1 1303 1301 NAG NAG . J 6 NAG A 1 1304 1302 NAG NAG . K 6 NAG A 1 1305 1303 NAG NAG . L 6 NAG A 1 1306 1304 NAG NAG . M 6 NAG A 1 1307 1305 NAG NAG . N 6 NAG A 1 1308 1306 NAG NAG . O 6 NAG A 1 1309 1307 NAG NAG . P 6 NAG A 1 1310 1308 NAG NAG . Q 6 NAG A 1 1311 1309 NAG NAG . R 6 NAG A 1 1312 1310 NAG NAG . S 6 NAG D 1 701 701 NAG NAG . T 6 NAG D 1 702 702 NAG NAG . U 6 NAG D 1 703 703 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 6 173.414 212.431 275.152 1 138.94 ? C1 NAG 1311 A 1 HETATM 2 C C2 NAG . . . Q 6 174.031 213.738 275.653 1 139.54 ? C2 NAG 1311 A 1 HETATM 3 C C3 NAG . . . Q 6 172.948 214.793 275.858 1 139.77 ? C3 NAG 1311 A 1 HETATM 4 C C4 NAG . . . Q 6 172.122 214.958 274.592 1 139.98 ? C4 NAG 1311 A 1 HETATM 5 C C5 NAG . . . Q 6 171.57 213.607 274.152 1 139.86 ? C5 NAG 1311 A 1 HETATM 6 C C6 NAG . . . Q 6 170.829 213.673 272.838 1 140.01 ? C6 NAG 1311 A 1 HETATM 7 C C7 NAG . . . Q 6 175.736 214.352 277.307 1 140.04 ? C7 NAG 1311 A 1 HETATM 8 C C8 NAG . . . Q 6 176.402 213.979 278.595 1 139.77 ? C8 NAG 1311 A 1 HETATM 9 N N2 NAG . . . Q 6 174.776 213.525 276.882 1 139.73 ? N2 NAG 1311 A 1 HETATM 10 O O3 NAG . . . Q 6 173.553 216.035 276.2 1 139.68 ? O3 NAG 1311 A 1 HETATM 11 O O4 NAG . . . Q 6 171.042 215.854 274.828 1 140.26 ? O4 NAG 1311 A 1 HETATM 12 O O5 NAG . . . Q 6 172.652 212.681 273.969 1 139.51 ? O5 NAG 1311 A 1 HETATM 13 O O6 NAG . . . Q 6 171.727 213.831 271.747 1 139.97 ? O6 NAG 1311 A 1 HETATM 14 O O7 NAG . . . Q 6 176.05 215.359 276.681 1 140.09 ? O7 NAG 1311 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #