data_2J25 # _model_server_result.job_id nz-L3HQZbsCIk8WJySYtiQ _model_server_result.datetime_utc '2024-11-16 19:37:01' _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 2j25 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1500}' # _entry.id 2J25 # _exptl.entry_id 2J25 _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 1 _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 2J25 _cell.length_a 108.626 _cell.length_b 280.821 _cell.length_c 91.064 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J25 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 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 PQS monomeric 1 author_and_software_defined_assembly 1 PQS monomeric 1 author_and_software_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,G,H,I,J,K,L,M,N,O,P,Y 1 1 B,D,E,F,Q,R,S,T,U,V,W,X,Z 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 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 5 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 4 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 2 n C NAG 1 C 1 NAG A 1498 NAG 2 n C NAG 2 C 2 NAG A 1499 NAG 3 n D NAG 1 D 1 NAG B 1498 NAG 3 n D NAG 2 D 2 NAG B 1499 NAG 3 n D BMA 3 D 3 BMA B 1500 BMA 3 n D MAN 4 D 4 MAN B 1501 MAN 3 n D MAN 5 D 5 MAN B 1502 MAN 4 n E NAG 1 E 1 NAG B 1503 NAG 4 n E NAG 2 E 2 NAG B 1504 NAG 4 n E BMA 3 E 3 BMA B 1505 BMA 2 n F NAG 1 F 1 NAG B 1506 NAG 2 n F NAG 2 F 2 NAG B 1507 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 4 A CYS 4 1_555 A SG CYS 16 A CYS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf2 A SG CYS 18 A CYS 18 1_555 A SG CYS 23 A CYS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? disulf ? disulf3 B SG CYS 4 B CYS 4 1_555 B SG CYS 16 B CYS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf4 B SG CYS 18 B CYS 18 1_555 B SG CYS 23 B CYS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? covale ? covale1 A ND2 ASN 19 A ASN 19 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 146 A ASN 146 1_555 G C1 NAG . A NAG 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? covale ? covale3 B ND2 ASN 19 B ASN 19 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B ND2 ASN 59 B ASN 59 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale5 B ND2 ASN 146 B ASN 146 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale8 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale10 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.506 ? covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _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 2J25 _atom_sites.fract_transf_matrix[1][1] 0.009206 _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] 0.003561 _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] 0.010981 _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 5 NAG A 1 1500 1500 NAG NAG . H 6 SO4 A 1 1501 1501 SO4 SO4 . I 6 SO4 A 1 1502 1502 SO4 SO4 . J 6 SO4 A 1 1503 1503 SO4 SO4 . K 6 SO4 A 1 1504 1504 SO4 SO4 . L 6 SO4 A 1 1505 1505 SO4 SO4 . M 6 SO4 A 1 1506 1506 SO4 SO4 . N 6 SO4 A 1 1507 1507 SO4 SO4 . O 6 SO4 A 1 1508 1508 SO4 SO4 . P 6 SO4 A 1 1509 1509 SO4 SO4 . Q 6 SO4 B 1 1508 1508 SO4 SO4 . R 6 SO4 B 1 1509 1509 SO4 SO4 . S 6 SO4 B 1 1510 1510 SO4 SO4 . T 6 SO4 B 1 1511 1511 SO4 SO4 . U 6 SO4 B 1 1512 1512 SO4 SO4 . V 6 SO4 B 1 1513 1513 SO4 SO4 . W 6 SO4 B 1 1514 1514 SO4 SO4 . X 6 SO4 B 1 1515 1515 SO4 SO4 . Y 7 HOH A 1 2001 2001 HOH HOH . Y 7 HOH A 2 2002 2002 HOH HOH . Y 7 HOH A 3 2003 2003 HOH HOH . Y 7 HOH A 4 2004 2004 HOH HOH . Y 7 HOH A 5 2005 2005 HOH HOH . Y 7 HOH A 6 2006 2006 HOH HOH . Y 7 HOH A 7 2007 2007 HOH HOH . Y 7 HOH A 8 2008 2008 HOH HOH . Y 7 HOH A 9 2009 2009 HOH HOH . Y 7 HOH A 10 2010 2010 HOH HOH . Y 7 HOH A 11 2011 2011 HOH HOH . Y 7 HOH A 12 2012 2012 HOH HOH . Y 7 HOH A 13 2013 2013 HOH HOH . Y 7 HOH A 14 2014 2014 HOH HOH . Y 7 HOH A 15 2015 2015 HOH HOH . Y 7 HOH A 16 2016 2016 HOH HOH . Y 7 HOH A 17 2017 2017 HOH HOH . Y 7 HOH A 18 2018 2018 HOH HOH . Y 7 HOH A 19 2019 2019 HOH HOH . Y 7 HOH A 20 2020 2020 HOH HOH . Y 7 HOH A 21 2021 2021 HOH HOH . Y 7 HOH A 22 2022 2022 HOH HOH . Y 7 HOH A 23 2023 2023 HOH HOH . Y 7 HOH A 24 2024 2024 HOH HOH . Y 7 HOH A 25 2025 2025 HOH HOH . Y 7 HOH A 26 2026 2026 HOH HOH . Y 7 HOH A 27 2027 2027 HOH HOH . Y 7 HOH A 28 2028 2028 HOH HOH . Y 7 HOH A 29 2029 2029 HOH HOH . Y 7 HOH A 30 2030 2030 HOH HOH . Y 7 HOH A 31 2031 2031 HOH HOH . Y 7 HOH A 32 2032 2032 HOH HOH . Y 7 HOH A 33 2033 2033 HOH HOH . Y 7 HOH A 34 2034 2034 HOH HOH . Y 7 HOH A 35 2035 2035 HOH HOH . Y 7 HOH A 36 2036 2036 HOH HOH . Y 7 HOH A 37 2037 2037 HOH HOH . Z 7 HOH B 1 2001 2001 HOH HOH . Z 7 HOH B 2 2002 2002 HOH HOH . Z 7 HOH B 3 2003 2003 HOH HOH . Z 7 HOH B 4 2004 2004 HOH HOH . Z 7 HOH B 5 2005 2005 HOH HOH . Z 7 HOH B 6 2006 2006 HOH HOH . Z 7 HOH B 7 2007 2007 HOH HOH . Z 7 HOH B 8 2008 2008 HOH HOH . Z 7 HOH B 9 2009 2009 HOH HOH . Z 7 HOH B 10 2010 2010 HOH HOH . Z 7 HOH B 11 2011 2011 HOH HOH . Z 7 HOH B 12 2012 2012 HOH HOH . Z 7 HOH B 13 2013 2013 HOH HOH . Z 7 HOH B 14 2014 2014 HOH HOH . Z 7 HOH B 15 2015 2015 HOH HOH . Z 7 HOH B 16 2016 2016 HOH HOH . Z 7 HOH B 17 2017 2017 HOH HOH . Z 7 HOH B 18 2018 2018 HOH HOH . Z 7 HOH B 19 2019 2019 HOH HOH . Z 7 HOH B 20 2020 2020 HOH HOH . Z 7 HOH B 21 2021 2021 HOH HOH . Z 7 HOH B 22 2022 2022 HOH HOH . Z 7 HOH B 23 2023 2023 HOH HOH . Z 7 HOH B 24 2024 2024 HOH HOH . Z 7 HOH B 25 2025 2025 HOH HOH . Z 7 HOH B 26 2026 2026 HOH HOH . Z 7 HOH B 27 2027 2027 HOH HOH . Z 7 HOH B 28 2028 2028 HOH HOH . Z 7 HOH B 29 2029 2029 HOH HOH . Z 7 HOH B 30 2030 2030 HOH HOH . Z 7 HOH B 31 2031 2031 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 . . . G 5 92.214 23.617 -14.13 1 55.62 ? C1 NAG 1500 A 1 HETATM 2 C C2 NAG . . . G 5 92.687 22.118 -14.368 1 58.26 ? C2 NAG 1500 A 1 HETATM 3 C C3 NAG . . . G 5 92.817 21.683 -15.835 1 59.74 ? C3 NAG 1500 A 1 HETATM 4 C C4 NAG . . . G 5 91.311 21.831 -16.368 1 60.71 ? C4 NAG 1500 A 1 HETATM 5 C C5 NAG . . . G 5 91.103 23.337 -16.381 1 59.34 ? C5 NAG 1500 A 1 HETATM 6 C C6 NAG . . . G 5 89.872 23.83 -17.153 1 58.73 ? C6 NAG 1500 A 1 HETATM 7 C C7 NAG . . . G 5 95.126 21.47 -13.663 1 58.05 ? C7 NAG 1500 A 1 HETATM 8 C C8 NAG . . . G 5 95.862 20.696 -12.628 1 57.09 ? C8 NAG 1500 A 1 HETATM 9 N N2 NAG . . . G 5 93.763 21.692 -13.431 1 58.34 ? N2 NAG 1500 A 1 HETATM 10 O O3 NAG . . . G 5 93.314 20.316 -15.949 1 60.02 ? O3 NAG 1500 A 1 HETATM 11 O O4 NAG . . . G 5 91.311 21.094 -17.688 1 62.89 ? O4 NAG 1500 A 1 HETATM 12 O O5 NAG . . . G 5 91.153 23.93 -15.045 1 57.41 ? O5 NAG 1500 A 1 HETATM 13 O O6 NAG . . . G 5 90.468 24.7 -18.096 1 57.89 ? O6 NAG 1500 A 1 HETATM 14 O O7 NAG . . . G 5 95.689 21.866 -14.717 1 57.57 ? O7 NAG 1500 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #