data_5LKR # _model_server_result.job_id 3lOX0vgeTiNpmJIfWeqKoA _model_server_result.datetime_utc '2024-11-18 10:23:53' _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 5lkr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":612}' # _entry.id 5LKR # _exptl.entry_id 5LKR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _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 5LKR _cell.length_a 73.681 _cell.length_b 79.463 _cell.length_c 228.869 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LKR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,K,L,M,N,O,P,Z 1 1 B,I,J,Q,R,S,T,U,V,W,X,Y,AA 2 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 x,y,z _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 ? 5 K N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T N N ? 5 U N N ? 5 X N N ? 5 Y N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 FUC NAG C1 O1 . O6 HO6 . sing 3 ? 4 2 1 FUL NAG 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 2 n C NAG 1 C 1 NAG A 602 NAG 2 n C NAG 2 C 2 NAG E 3 NAG 2 n D NAG 1 D 1 NAG A 604 NAG 2 n D NAG 2 D 2 NAG A 605 NAG 3 n E NAG 1 E 1 NAG A 606 NAG 3 n E FUC 2 E 2 FUC A 607 FUC 2 n F NAG 1 F 1 NAG A 608 NAG 2 n F NAG 2 F 2 NAG A 609 NAG 2 n G NAG 1 G 1 NAG A 611 NAG 2 n G NAG 2 G 2 NAG A 612 NAG 2 n H NAG 1 H 1 NAG A 613 NAG 2 n H NAG 2 H 2 NAG A 614 NAG 2 n I NAG 1 I 1 NAG B 603 NAG 2 n I NAG 2 I 2 NAG B 604 NAG 4 n J NAG 1 J 1 NAG B 605 NAG 4 n J FUL 2 J 2 FUL B 606 FUL # 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 65 A CYS 65 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 252 A CYS 252 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 400 A CYS 400 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf4 B SG CYS 65 B CYS 65 1_555 B SG CYS 92 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf5 B SG CYS 252 B CYS 252 1_555 B SG CYS 263 B CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf6 B SG CYS 400 B CYS 400 1_555 B SG CYS 519 B CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? covale ? covale1 A ND2 ASN 17 A ASN 17 1_555 K C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 57 A ASN 57 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 106 A ASN 106 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale4 A ND2 ASN 241 A ASN 241 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 A ND2 ASN 341 A ASN 341 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 A ND2 ASN 481 A ASN 481 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 A ND2 ASN 486 A ASN 486 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 B ND2 ASN 17 B ASN 17 1_555 Y C1 NAG . B NAG 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale9 B ND2 ASN 57 B ASN 57 1_555 Q C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 B ND2 ASN 106 B ASN 106 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale11 B ND2 ASN 241 B ASN 241 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale12 B ND2 ASN 256 B ASN 256 1_555 S C1 NAG . B NAG 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale13 B ND2 ASN 341 B ASN 341 1_555 T C1 NAG . B NAG 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale14 B ND2 ASN 481 B ASN 481 1_555 U C1 NAG . B NAG 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale15 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale16 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale17 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale18 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale19 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale20 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale21 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale22 J O6 NAG . J NAG 1 1_555 J C1 FUL . J FUL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? # _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 353 n n C1 O1 NAG sing 354 n n C1 O5 NAG sing 355 n n C1 H1 NAG sing 356 n n C2 C3 NAG sing 357 n n C2 N2 NAG sing 358 n n C2 H2 NAG sing 359 n n C3 C4 NAG sing 360 n n C3 O3 NAG sing 361 n n C3 H3 NAG sing 362 n n C4 C5 NAG sing 363 n n C4 O4 NAG sing 364 n n C4 H4 NAG sing 365 n n C5 C6 NAG sing 366 n n C5 O5 NAG sing 367 n n C5 H5 NAG sing 368 n n C6 O6 NAG sing 369 n n C6 H61 NAG sing 370 n n C6 H62 NAG sing 371 n n C7 C8 NAG sing 372 n n C7 N2 NAG sing 373 n n C7 O7 NAG doub 374 n n C8 H81 NAG sing 375 n n C8 H82 NAG sing 376 n n C8 H83 NAG sing 377 n n N2 HN2 NAG sing 378 n n O1 HO1 NAG sing 379 n n O3 HO3 NAG sing 380 n n O4 HO4 NAG sing 381 n n O6 HO6 NAG sing 382 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 5LKR _atom_sites.fract_transf_matrix[1][1] 0.013572 _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] 0.012584 _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] 0.004369 _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 5 NAG A 1 601 601 NAG NAG . L 6 FUL A 1 604 603 FUL FUL . M 7 GOL A 1 615 616 GOL GOL . N 8 6YC A 1 616 1 6YC DRG . O 7 GOL A 1 617 1 GOL GOL . P 9 PEG A 1 618 1 PEG PEG . Q 5 NAG B 1 601 602 NAG NAG . R 5 NAG B 1 606 607 NAG NAG . S 5 NAG B 1 607 608 NAG NAG . T 5 NAG B 1 608 609 NAG NAG . U 5 NAG B 1 609 610 NAG NAG . V 7 GOL B 1 610 612 GOL GOL . W 8 6YC B 1 611 2 6YC DRG . X 5 NAG B 1 612 1 NAG NAG . Y 5 NAG B 1 613 2 NAG NAG . Z 10 HOH A 1 701 36 HOH HOH . Z 10 HOH A 2 702 16 HOH HOH . Z 10 HOH A 3 703 4 HOH HOH . Z 10 HOH A 4 704 42 HOH HOH . Z 10 HOH A 5 705 39 HOH HOH . Z 10 HOH A 6 706 28 HOH HOH . Z 10 HOH A 7 707 38 HOH HOH . Z 10 HOH A 8 708 7 HOH HOH . Z 10 HOH A 9 709 10 HOH HOH . Z 10 HOH A 10 710 41 HOH HOH . Z 10 HOH A 11 711 17 HOH HOH . Z 10 HOH A 12 712 30 HOH HOH . Z 10 HOH A 13 713 40 HOH HOH . Z 10 HOH A 14 714 37 HOH HOH . Z 10 HOH A 15 715 25 HOH HOH . AA 10 HOH B 1 701 33 HOH HOH . AA 10 HOH B 2 702 1 HOH HOH . AA 10 HOH B 3 703 22 HOH HOH . AA 10 HOH B 4 704 18 HOH HOH . AA 10 HOH B 5 705 20 HOH HOH . AA 10 HOH B 6 706 27 HOH HOH . AA 10 HOH B 7 707 2 HOH HOH . AA 10 HOH B 8 708 15 HOH HOH . AA 10 HOH B 9 709 11 HOH HOH . AA 10 HOH B 10 710 6 HOH HOH . AA 10 HOH B 11 711 5 HOH HOH . AA 10 HOH B 12 712 21 HOH HOH . AA 10 HOH B 13 713 3 HOH HOH . AA 10 HOH B 14 714 31 HOH HOH . AA 10 HOH B 15 715 13 HOH HOH . AA 10 HOH B 16 716 32 HOH HOH . AA 10 HOH B 17 717 19 HOH HOH . AA 10 HOH B 18 718 12 HOH HOH . AA 10 HOH B 19 719 14 HOH HOH . AA 10 HOH B 20 720 34 HOH HOH . AA 10 HOH B 21 721 9 HOH HOH . # 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 . . . X 5 -28.673 -4.942 -25.647 1 100.37 ? C1 NAG 612 B 1 HETATM 2 C C2 NAG . . . X 5 -29.423 -4.572 -24.352 1 114.19 ? C2 NAG 612 B 1 HETATM 3 C C3 NAG . . . X 5 -28.612 -3.577 -23.492 1 112.83 ? C3 NAG 612 B 1 HETATM 4 C C4 NAG . . . X 5 -27.126 -3.918 -23.437 1 105.72 ? C4 NAG 612 B 1 HETATM 5 C C5 NAG . . . X 5 -26.617 -4.193 -24.84 1 104.18 ? C5 NAG 612 B 1 HETATM 6 C C6 NAG . . . X 5 -25.15 -4.551 -24.916 1 100.27 ? C6 NAG 612 B 1 HETATM 7 C C7 NAG . . . X 5 -31.69 -4.628 -25.349 1 120.77 ? C7 NAG 612 B 1 HETATM 8 C C8 NAG . . . X 5 -32.931 -3.824 -25.608 1 90.78 ? C8 NAG 612 B 1 HETATM 9 N N2 NAG . . . X 5 -30.715 -3.991 -24.688 1 127.2 ? N2 NAG 612 B 1 HETATM 10 O O3 NAG . . . X 5 -29.146 -3.554 -22.172 1 109.81 ? O3 NAG 612 B 1 HETATM 11 O O4 NAG . . . X 5 -26.398 -2.839 -22.862 1 115.02 ? O4 NAG 612 B 1 HETATM 12 O O5 NAG . . . X 5 -27.355 -5.305 -25.348 1 102.11 ? O5 NAG 612 B 1 HETATM 13 O O6 NAG . . . X 5 -24.548 -4.009 -26.086 1 85.27 ? O6 NAG 612 B 1 HETATM 14 O O7 NAG . . . X 5 -31.587 -5.803 -25.706 1 111.21 ? O7 NAG 612 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 472 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #