data_2JBK # _model_server_result.job_id XEFtSM4YOYwWQxJmQPHnFA _model_server_result.datetime_utc '2024-10-18 16:29:21' _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 2jbk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1757}' # _entry.id 2JBK # _exptl.entry_id 2JBK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 2JBK _cell.length_a 103.144 _cell.length_b 130.758 _cell.length_c 159.992 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JBK _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 130.758 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 J N N ? 7 K N N ? 7 L N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . 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 B NAG 1 B 1 NAG A 1751 NAG 2 n B NAG 2 B 2 NAG A 1752 NAG 2 n C NAG 1 C 1 NAG A 1754 NAG 2 n C NAG 2 C 2 NAG A 1755 NAG 2 n D NAG 1 D 1 NAG A 1758 NAG 2 n D NAG 2 D 2 NAG A 1759 NAG 3 n E NAG 1 E 1 NAG A 1760 NAG 3 n E NAG 2 E 2 NAG A 1761 NAG 3 n E BMA 3 E 3 BMA A 1762 BMA 3 n E MAN 4 E 4 MAN A 1763 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 covale ? covale1 A ND2 ASN 33 A ASN 76 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 78 A ASN 121 1_555 J C1 NAG . A NAG 1753 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale3 A ND2 ASN 97 A ASN 140 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 A ND2 ASN 152 A ASN 195 1_555 K C1 NAG . A NAG 1756 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? covale ? covale5 A ND2 ASN 416 A ASN 459 1_555 L C1 NAG . A NAG 1757 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale6 A ND2 ASN 433 A ASN 476 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 A ND2 ASN 595 A ASN 638 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale13 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 A O THR 226 A THR 269 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc2 A OG1 THR 226 A THR 269 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 A O TYR 229 A TYR 272 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc4 A NE2 HIS 334 A HIS 377 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? metalc ? metalc5 A OD2 ASP 344 A ASP 387 1_555 F ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc6 A OD1 ASP 344 A ASP 387 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc7 A OE2 GLU 382 A GLU 425 1_555 F ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc8 A OE1 GLU 390 A GLU 433 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc9 A OE2 GLU 390 A GLU 433 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc10 A OE2 GLU 393 A GLU 436 1_555 H CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc11 A OD2 ASP 410 A ASP 453 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc12 A NE2 HIS 510 A HIS 553 1_555 F ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc13 F ZN ZN . A ZN 801 1_555 N O HOH . A HOH 2018 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc14 G ZN ZN . A ZN 802 1_555 N O HOH . A HOH 2018 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 2JBK _atom_sites.fract_transf_matrix[1][1] 0.009695 _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] 0.007648 _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] 0.00625 _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 F 4 ZN A 1 801 801 ZN ZN . G 4 ZN A 1 802 802 ZN ZN . H 5 CA A 1 803 803 CA CA . I 6 CL A 1 804 804 CL CL . J 7 NAG A 1 1753 1753 NAG NAG . K 7 NAG A 1 1756 1756 NAG NAG . L 7 NAG A 1 1757 1757 NAG NAG . M 8 QUS A 1 1764 1764 QUS QUS . N 9 HOH A 1 2001 2001 HOH HOH . N 9 HOH A 2 2002 2002 HOH HOH . N 9 HOH A 3 2003 2003 HOH HOH . N 9 HOH A 4 2004 2004 HOH HOH . N 9 HOH A 5 2005 2005 HOH HOH . N 9 HOH A 6 2006 2006 HOH HOH . N 9 HOH A 7 2007 2007 HOH HOH . N 9 HOH A 8 2008 2008 HOH HOH . N 9 HOH A 9 2009 2009 HOH HOH . N 9 HOH A 10 2010 2010 HOH HOH . N 9 HOH A 11 2011 2011 HOH HOH . N 9 HOH A 12 2012 2012 HOH HOH . N 9 HOH A 13 2013 2013 HOH HOH . N 9 HOH A 14 2014 2014 HOH HOH . N 9 HOH A 15 2015 2015 HOH HOH . N 9 HOH A 16 2016 2016 HOH HOH . N 9 HOH A 17 2017 2017 HOH HOH . N 9 HOH A 18 2018 2018 HOH HOH . N 9 HOH A 19 2019 2019 HOH HOH . N 9 HOH A 20 2020 2020 HOH HOH . N 9 HOH A 21 2021 2021 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 . . . L 7 35.795 37.404 53.82 1 35 ? C1 NAG 1757 A 1 HETATM 2 C C2 NAG . . . L 7 35.784 37.648 52.308 1 35 ? C2 NAG 1757 A 1 HETATM 3 C C3 NAG . . . L 7 37.089 37.193 51.635 1 35 ? C3 NAG 1757 A 1 HETATM 4 C C4 NAG . . . L 7 38.115 38.116 52.285 1 35 ? C4 NAG 1757 A 1 HETATM 5 C C5 NAG . . . L 7 38.301 37.784 53.797 1 35 ? C5 NAG 1757 A 1 HETATM 6 C C6 NAG . . . L 7 38.76 39.067 54.536 1 35 ? C6 NAG 1757 A 1 HETATM 7 C C7 NAG . . . L 7 34.27 37.631 50.401 1 35 ? C7 NAG 1757 A 1 HETATM 8 C C8 NAG . . . L 7 33.517 36.591 49.63 1 35 ? C8 NAG 1757 A 1 HETATM 9 N N2 NAG . . . L 7 34.509 37.245 51.69 1 35 ? N2 NAG 1757 A 1 HETATM 10 O O3 NAG . . . L 7 37.09 37.427 50.237 1 35 ? O3 NAG 1757 A 1 HETATM 11 O O4 NAG . . . L 7 39.367 38.103 51.601 1 35 ? O4 NAG 1757 A 1 HETATM 12 O O5 NAG . . . L 7 37.131 37.162 54.399 1 35 ? O5 NAG 1757 A 1 HETATM 13 O O6 NAG . . . L 7 39.183 40.093 53.618 1 35 ? O6 NAG 1757 A 1 HETATM 14 O O7 NAG . . . L 7 34.62 38.701 49.854 1 35 ? O7 NAG 1757 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #