data_1GHG # _entry.id 1GHG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1GHG pdb_00001ghg 10.2210/pdb1ghg/pdb RCSB RCSB001516 ? ? WWPDB D_1000001516 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2001-02-12 2 'Structure model' 1 1 2011-06-14 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-07-27 5 'Structure model' 1 4 2012-12-12 6 'Structure model' 1 5 2017-10-04 7 'Structure model' 2 0 2023-12-27 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Non-polymer description' 7 4 'Structure model' 'Structure summary' 8 5 'Structure model' Other 9 6 'Structure model' 'Refinement description' 10 7 'Structure model' 'Data collection' 11 7 'Structure model' 'Database references' 12 7 'Structure model' 'Derived calculations' 13 7 'Structure model' 'Polymer sequence' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 6 'Structure model' software 2 7 'Structure model' chem_comp_atom 3 7 'Structure model' chem_comp_bond 4 7 'Structure model' database_2 5 7 'Structure model' entity_poly 6 7 'Structure model' struct_conn 7 7 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 7 'Structure model' '_database_2.pdbx_DOI' 2 7 'Structure model' '_database_2.pdbx_database_accession' 3 7 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 4 7 'Structure model' '_struct_conn.pdbx_dist_value' 5 7 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 7 'Structure model' '_struct_conn.ptnr1_label_atom_id' 7 7 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 8 7 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 9 7 'Structure model' '_struct_conn.ptnr2_label_atom_id' 10 7 'Structure model' '_struct_conn.ptnr2_label_comp_id' 11 7 'Structure model' '_struct_conn.ptnr2_label_seq_id' 12 7 'Structure model' '_struct_site.pdbx_auth_asym_id' 13 7 'Structure model' '_struct_site.pdbx_auth_comp_id' 14 7 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 1GHG _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2000-12-13 _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1AA5 unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN' PDB 1C0Q unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH 2-ACETOXY-D-PROPANOIC ACID' PDB 1C0R unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN WITH D-LACTIC ACID' PDB 1FVM unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH DI-ACETYL-LYS-D-ALA-D-ALA' PDB 1GAC unspecified 'SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT' PDB 1PN3 unspecified 'CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXD WITH TDP AND DESVANCOSAMINYL VANCOMYCIN' PDB 1PNV unspecified 'CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXED WITH TDP AND VANCOMYCIN' PDB 1QD8 unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL GLYCIN' PDB 1RRV unspecified 'CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEXED WITH TDP AND DESVANCOSAMINYL VANCOMYCIN.' PDB 1SHO unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN' # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kaplan, J.' 1 'Korty, B.D.' 2 'Axelsen, P.H.' 3 'Loll, P.J.' 4 # _citation.id primary _citation.title 'The Role of Sugar Residues in Molecular Recognition by Vancomycin' _citation.journal_abbrev J.Med.Chem. _citation.journal_volume 44 _citation.page_first 1837 _citation.page_last ? _citation.year 2001 _citation.journal_id_ASTM JMCMAR _citation.country US _citation.journal_id_ISSN 0022-2623 _citation.journal_id_CSD 0151 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11356118 _citation.pdbx_database_id_DOI 10.1021/JM0005306 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kaplan, J.' 1 ? primary 'Korty, B.D.' 2 ? primary 'Axelsen, P.H.' 3 ? primary 'Loll, P.J.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'VANCOMYCIN AGLYCON' 1149.977 4 ? ? ? ? 2 non-polymer syn 'ACETIC ACID' 60.052 4 ? ? ? ? 3 non-polymer syn 'DIMETHYL SULFOXIDE' 78.133 2 ? ? ? ? 4 water nat water 18.015 67 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(MLU)(OMZ)N(GHP)(GHP)(OMY)(3FG)' _entity_poly.pdbx_seq_one_letter_code_can XXNGGYX _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ACETIC ACID' ACY 3 'DIMETHYL SULFOXIDE' DMS 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MLU n 1 2 OMZ n 1 3 ASN n 1 4 GHP n 1 5 GHP n 1 6 OMY n 1 7 3FG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'AMYCOLATOPSIS ORIENTALIS' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 31958 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 3FG 'L-peptide linking' . '(2S)-amino(3,5-dihydroxyphenyl)ethanoic acid' ? 'C8 H9 N O4' 183.161 ACY non-polymer . 'ACETIC ACID' ? 'C2 H4 O2' 60.052 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 DMS non-polymer . 'DIMETHYL SULFOXIDE' ? 'C2 H6 O S' 78.133 GHP 'D-peptide linking' . '(2R)-amino(4-hydroxyphenyl)ethanoic acid' ? 'C8 H9 N O3' 167.162 HOH non-polymer . WATER ? 'H2 O' 18.015 MLU 'D-peptide linking' . N-methyl-D-leucine ? 'C7 H15 N O2' 145.199 OMY 'L-peptide linking' n '(betaR)-3-chloro-beta-hydroxy-L-tyrosine' ? 'C9 H10 Cl N O4' 231.633 OMZ 'D-peptide linking' . '(betaR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE' ? 'C9 H10 Cl N O4' 231.633 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MLU 1 1 1 MLU MLU A . n A 1 2 OMZ 2 2 2 OMZ OMZ A . n A 1 3 ASN 3 3 3 ASN ASN A . n A 1 4 GHP 4 4 4 GHP GHP A . n A 1 5 GHP 5 5 5 GHP GHP A . n A 1 6 OMY 6 6 6 OMY OMY A . n A 1 7 3FG 7 7 7 3FG 3FG A . n B 1 1 MLU 1 1 1 MLU MLU B . n B 1 2 OMZ 2 2 2 OMZ OMZ B . n B 1 3 ASN 3 3 3 ASN ASN B . n B 1 4 GHP 4 4 4 GHP GHP B . n B 1 5 GHP 5 5 5 GHP GHP B . n B 1 6 OMY 6 6 6 OMY OMY B . n B 1 7 3FG 7 7 7 3FG 3FG B . n C 1 1 MLU 1 1 1 MLU MLU C . n C 1 2 OMZ 2 2 2 OMZ OMZ C . n C 1 3 ASN 3 3 3 ASN ASN C . n C 1 4 GHP 4 4 4 GHP GHP C . n C 1 5 GHP 5 5 5 GHP GHP C . n C 1 6 OMY 6 6 6 OMY OMY C . n C 1 7 3FG 7 7 7 3FG 3FG C . n D 1 1 MLU 1 1 1 MLU MLU D . n D 1 2 OMZ 2 2 2 OMZ OMZ D . n D 1 3 ASN 3 3 3 ASN ASN D . n D 1 4 GHP 4 4 4 GHP GHP D . n D 1 5 GHP 5 5 5 GHP GHP D . n D 1 6 OMY 6 6 6 OMY OMY D . n D 1 7 3FG 7 7 7 3FG 3FG D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_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_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 ACY 1 11 11 ACY ACY A . F 2 ACY 1 11 11 ACY ACY B . G 2 ACY 1 11 11 ACY ACY C . H 3 DMS 1 12 12 DMS DMS C . I 2 ACY 1 11 11 ACY ACY D . J 3 DMS 1 12 12 DMS DMS D . K 4 HOH 1 2001 2001 HOH HOH A . K 4 HOH 2 2002 2002 HOH HOH A . K 4 HOH 3 2003 2003 HOH HOH A . K 4 HOH 4 2004 2004 HOH HOH A . K 4 HOH 5 2005 2005 HOH HOH A . K 4 HOH 6 2006 2006 HOH HOH A . K 4 HOH 7 2007 2007 HOH HOH A . K 4 HOH 8 2008 2008 HOH HOH A . K 4 HOH 9 2009 2009 HOH HOH A . K 4 HOH 10 2010 2010 HOH HOH A . K 4 HOH 11 2011 2011 HOH HOH A . K 4 HOH 12 2012 2012 HOH HOH A . K 4 HOH 13 2013 2013 HOH HOH A . K 4 HOH 14 2014 2014 HOH HOH A . K 4 HOH 15 2015 2015 HOH HOH A . K 4 HOH 16 2016 2016 HOH HOH A . K 4 HOH 17 2017 2017 HOH HOH A . K 4 HOH 18 2018 2018 HOH HOH A . L 4 HOH 1 2001 2001 HOH HOH B . L 4 HOH 2 2002 2002 HOH HOH B . L 4 HOH 3 2003 2003 HOH HOH B . L 4 HOH 4 2004 2004 HOH HOH B . L 4 HOH 5 2005 2005 HOH HOH B . L 4 HOH 6 2006 2006 HOH HOH B . L 4 HOH 7 2007 2007 HOH HOH B . L 4 HOH 8 2008 2008 HOH HOH B . L 4 HOH 9 2009 2009 HOH HOH B . L 4 HOH 10 2010 2010 HOH HOH B . L 4 HOH 11 2011 2011 HOH HOH B . L 4 HOH 12 2012 2012 HOH HOH B . L 4 HOH 13 2013 2013 HOH HOH B . L 4 HOH 14 2014 2014 HOH HOH B . L 4 HOH 15 2015 2015 HOH HOH B . M 4 HOH 1 2001 2001 HOH HOH C . M 4 HOH 2 2002 2002 HOH HOH C . M 4 HOH 3 2003 2003 HOH HOH C . M 4 HOH 4 2004 2004 HOH HOH C . M 4 HOH 5 2005 2005 HOH HOH C . M 4 HOH 6 2006 2006 HOH HOH C . M 4 HOH 7 2007 2007 HOH HOH C . M 4 HOH 8 2008 2008 HOH HOH C . M 4 HOH 9 2009 2009 HOH HOH C . M 4 HOH 10 2010 2010 HOH HOH C . M 4 HOH 11 2011 2011 HOH HOH C . M 4 HOH 12 2012 2012 HOH HOH C . M 4 HOH 13 2013 2013 HOH HOH C . M 4 HOH 14 2014 2014 HOH HOH C . M 4 HOH 15 2015 2015 HOH HOH C . M 4 HOH 16 2016 2016 HOH HOH C . M 4 HOH 17 2017 2017 HOH HOH C . M 4 HOH 18 2018 2018 HOH HOH C . M 4 HOH 19 2019 2019 HOH HOH C . N 4 HOH 1 2001 2001 HOH HOH D . N 4 HOH 2 2002 2002 HOH HOH D . N 4 HOH 3 2003 2003 HOH HOH D . N 4 HOH 4 2004 2004 HOH HOH D . N 4 HOH 5 2005 2005 HOH HOH D . N 4 HOH 6 2006 2006 HOH HOH D . N 4 HOH 7 2007 2007 HOH HOH D . N 4 HOH 8 2008 2008 HOH HOH D . N 4 HOH 9 2009 2009 HOH HOH D . N 4 HOH 10 2010 2010 HOH HOH D . N 4 HOH 11 2011 2011 HOH HOH D . N 4 HOH 12 2012 2012 HOH HOH D . N 4 HOH 13 2013 2013 HOH HOH D . N 4 HOH 14 2014 2014 HOH HOH D . N 4 HOH 15 2015 2015 HOH HOH D . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SnB phasing . ? 1 SHELXL refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 1GHG _cell.length_a 29.480 _cell.length_b 29.480 _cell.length_c 74.270 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GHG _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 # _exptl.entry_id 1GHG _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.75 _exptl_crystal.density_percent_sol 29.87 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.9 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '100 MM SODIUM CACODYLATE, 1.6 M SODIUM ACETATE, PH 6.9, VAPOR DIFFUSION/HANGING DROP, TEMPERATURE 277K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 1998-02-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.978 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X12B' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X12B _diffrn_source.pdbx_wavelength 0.978 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 1GHG _reflns.observed_criterion_sigma_I 2.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 8.000 _reflns.d_resolution_high 0.980 _reflns.number_obs 16377 _reflns.number_all ? _reflns.percent_possible_obs 87.2 _reflns.pdbx_Rmerge_I_obs 0.05200 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 29.8000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.400 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 0.98 _reflns_shell.d_res_low 1.08 _reflns_shell.percent_possible_all 66.7 _reflns_shell.Rmerge_I_obs 0.23800 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 5.80 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 1GHG _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 17071 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 4.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.00 _refine.ls_d_res_high 0.98 _refine.ls_percent_reflns_obs 90.9 _refine.ls_R_factor_obs 0.150 _refine.ls_R_factor_all 0.150 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.150 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 8.300 _refine.ls_number_reflns_R_free 1422 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details 'CONJUGATE GRADIENT FOR MOST OF REFINEMENT, FOLLOWED BY BLOCKED LEAST SQUARES' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ;THE FOUR COPIES OF THE MOLECULE IN THE ASYMMETRIC UNIT WERE RESTRAINED TO HAVE SIMLAR 1,2- AND 1,3-DISTANCES. SP2 CENTERS AND RINGS WERE RESTRAINED TO PLANARITY. ; _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 320 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 24 _refine_hist.number_atoms_solvent 67 _refine_hist.number_atoms_total 411 _refine_hist.d_res_high 0.98 _refine_hist.d_res_low 8.00 # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 1GHG _pdbx_refine.R_factor_all_no_cutoff 0.150 _pdbx_refine.R_factor_obs_no_cutoff 0.150 _pdbx_refine.free_R_factor_no_cutoff 0.150 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 8.300 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1422 _pdbx_refine.R_factor_all_4sig_cutoff 0.142 _pdbx_refine.R_factor_obs_4sig_cutoff 0.142 _pdbx_refine.free_R_factor_4sig_cutoff 0.142 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 8.300 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 1331 _pdbx_refine.number_reflns_obs_4sig_cutoff 15912 # _database_PDB_matrix.entry_id 1GHG _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1GHG _struct.title 'CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1GHG _struct_keywords.pdbx_keywords ANTIBIOTIC _struct_keywords.text 'GLYCOPEPTIDE, ANTIBIOTIC, AGLYCON, VANCOMYCIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 3 ? I N N 2 ? J N N 3 ? K N N 4 ? L N N 4 ? M N N 4 ? N N N 4 ? # _struct_ref.id 1 _struct_ref.db_name NOR _struct_ref.db_code NOR00681 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession NOR00681 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1GHG A 1 ? 7 ? NOR00681 1 ? 7 ? 1 7 2 1 1GHG B 1 ? 7 ? NOR00681 1 ? 7 ? 1 7 3 1 1GHG C 1 ? 7 ? NOR00681 1 ? 7 ? 1 7 4 1 1GHG D 1 ? 7 ? NOR00681 1 ? 7 ? 1 7 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,K,L 2 1 C,D,G,H,I,J,M,N # _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] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_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_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A MLU 1 C ? ? ? 1_555 A OMZ 2 N ? ? A MLU 1 A OMZ 2 1_555 ? ? ? ? ? ? ? 1.347 ? ? covale2 covale both ? A OMZ 2 C ? ? ? 1_555 A ASN 3 N ? ? A OMZ 2 A ASN 3 1_555 ? ? ? ? ? ? ? 1.387 ? ? covale3 covale none ? A OMZ 2 OH ? ? ? 1_555 A GHP 4 C5 ? ? A OMZ 2 A GHP 4 1_555 ? ? ? ? ? ? ? 1.417 ? ? covale4 covale both ? A ASN 3 C ? ? ? 1_555 A GHP 4 N ? ? A ASN 3 A GHP 4 1_555 ? ? ? ? ? ? ? 1.357 ? ? covale5 covale both ? A GHP 4 C ? ? ? 1_555 A GHP 5 N ? ? A GHP 4 A GHP 5 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale6 covale none ? A GHP 4 C3 ? ? ? 1_555 A OMY 6 OCZ ? ? A GHP 4 A OMY 6 1_555 ? ? ? ? ? ? ? 1.412 ? ? covale7 covale both ? A GHP 5 C ? ? ? 1_555 A OMY 6 N ? ? A GHP 5 A OMY 6 1_555 ? ? ? ? ? ? ? 1.352 ? ? covale8 covale one ? A GHP 5 C3 ? ? ? 1_555 A 3FG 7 CG1 ? ? A GHP 5 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.521 ? ? covale9 covale both ? A OMY 6 C ? ? ? 1_555 A 3FG 7 N ? ? A OMY 6 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.348 ? ? covale10 covale both ? B MLU 1 C ? ? ? 1_555 B OMZ 2 N ? ? B MLU 1 B OMZ 2 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale11 covale both ? B OMZ 2 C ? ? ? 1_555 B ASN 3 N ? ? B OMZ 2 B ASN 3 1_555 ? ? ? ? ? ? ? 1.394 ? ? covale12 covale none ? B OMZ 2 OH ? ? ? 1_555 B GHP 4 C5 ? ? B OMZ 2 B GHP 4 1_555 ? ? ? ? ? ? ? 1.411 ? ? covale13 covale both ? B ASN 3 C ? ? ? 1_555 B GHP 4 N ? ? B ASN 3 B GHP 4 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale14 covale both ? B GHP 4 C ? ? ? 1_555 B GHP 5 N ? ? B GHP 4 B GHP 5 1_555 ? ? ? ? ? ? ? 1.348 ? ? covale15 covale none ? B GHP 4 C3 ? ? ? 1_555 B OMY 6 OCZ ? ? B GHP 4 B OMY 6 1_555 ? ? ? ? ? ? ? 1.402 ? ? covale16 covale both ? B GHP 5 C ? ? ? 1_555 B OMY 6 N ? ? B GHP 5 B OMY 6 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale17 covale one ? B GHP 5 C3 ? ? ? 1_555 B 3FG 7 CG1 ? ? B GHP 5 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.490 ? ? covale18 covale both ? B OMY 6 C ? ? ? 1_555 B 3FG 7 N ? ? B OMY 6 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale19 covale both ? C MLU 1 C ? ? ? 1_555 C OMZ 2 N ? ? C MLU 1 C OMZ 2 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale20 covale both ? C OMZ 2 C ? ? ? 1_555 C ASN 3 N ? ? C OMZ 2 C ASN 3 1_555 ? ? ? ? ? ? ? 1.353 ? ? covale21 covale none ? C OMZ 2 OH ? ? ? 1_555 C GHP 4 C5 ? ? C OMZ 2 C GHP 4 1_555 ? ? ? ? ? ? ? 1.376 ? ? covale22 covale both ? C ASN 3 C ? ? ? 1_555 C GHP 4 N ? ? C ASN 3 C GHP 4 1_555 ? ? ? ? ? ? ? 1.310 ? ? covale23 covale both ? C GHP 4 C ? ? ? 1_555 C GHP 5 N ? ? C GHP 4 C GHP 5 1_555 ? ? ? ? ? ? ? 1.343 ? ? covale24 covale none ? C GHP 4 C3 ? ? ? 1_555 C OMY 6 OCZ ? ? C GHP 4 C OMY 6 1_555 ? ? ? ? ? ? ? 1.428 ? ? covale25 covale both ? C GHP 5 C ? ? ? 1_555 C OMY 6 N ? ? C GHP 5 C OMY 6 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale26 covale one ? C GHP 5 C3 ? ? ? 1_555 C 3FG 7 CG1 ? ? C GHP 5 C 3FG 7 1_555 ? ? ? ? ? ? ? 1.485 ? ? covale27 covale both ? C OMY 6 C ? ? ? 1_555 C 3FG 7 N ? ? C OMY 6 C 3FG 7 1_555 ? ? ? ? ? ? ? 1.353 ? ? covale28 covale both ? D MLU 1 C ? ? ? 1_555 D OMZ 2 N ? ? D MLU 1 D OMZ 2 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale29 covale both ? D OMZ 2 C ? ? ? 1_555 D ASN 3 N ? ? D OMZ 2 D ASN 3 1_555 ? ? ? ? ? ? ? 1.355 ? ? covale30 covale none ? D OMZ 2 OH ? ? ? 1_555 D GHP 4 C5 ? ? D OMZ 2 D GHP 4 1_555 ? ? ? ? ? ? ? 1.406 ? ? covale31 covale both ? D ASN 3 C ? ? ? 1_555 D GHP 4 N ? ? D ASN 3 D GHP 4 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale32 covale both ? D GHP 4 C ? ? ? 1_555 D GHP 5 N ? ? D GHP 4 D GHP 5 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale33 covale none ? D GHP 4 C3 ? ? ? 1_555 D OMY 6 OCZ ? ? D GHP 4 D OMY 6 1_555 ? ? ? ? ? ? ? 1.420 ? ? covale34 covale both ? D GHP 5 C ? ? ? 1_555 D OMY 6 N ? ? D GHP 5 D OMY 6 1_555 ? ? ? ? ? ? ? 1.278 ? ? covale35 covale one ? D GHP 5 C3 ? ? ? 1_555 D 3FG 7 CG1 ? ? D GHP 5 D 3FG 7 1_555 ? ? ? ? ? ? ? 1.467 ? ? covale36 covale both ? D OMY 6 C ? ? ? 1_555 D 3FG 7 N ? ? D OMY 6 D 3FG 7 1_555 ? ? ? ? ? ? ? 1.363 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GHP 5 A . ? GHP 5 A OMY 6 A ? OMY 6 A 1 11.50 2 GHP 5 B . ? GHP 5 B OMY 6 B ? OMY 6 B 1 11.15 3 GHP 5 C . ? GHP 5 C OMY 6 C ? OMY 6 C 1 9.42 4 GHP 5 D . ? GHP 5 D OMY 6 D ? OMY 6 D 1 5.63 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A ACY 11 ? 6 'BINDING SITE FOR RESIDUE ACY A 11' AC2 Software B ACY 11 ? 7 'BINDING SITE FOR RESIDUE ACY B 11' AC3 Software C ACY 11 ? 7 'BINDING SITE FOR RESIDUE ACY C 11' AC4 Software C DMS 12 ? 5 'BINDING SITE FOR RESIDUE DMS C 12' AC5 Software D ACY 11 ? 6 'BINDING SITE FOR RESIDUE ACY D 11' AC6 Software D DMS 12 ? 5 'BINDING SITE FOR RESIDUE DMS D 12' AC7 Software ? ? ? ? 35 'BINDING SITE FOR CHAIN A OF VANCOMYCIN AGLYCONE' AC8 Software ? ? ? ? 38 'BINDING SITE FOR CHAIN B OF VANCOMYCIN AGLYCONE' AC9 Software ? ? ? ? 36 'BINDING SITE FOR CHAIN C OF VANCOMYCIN AGLYCONE' BC1 Software ? ? ? ? 40 'BINDING SITE FOR CHAIN D OF VANCOMYCIN AGLYCONE' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 MLU A 1 ? MLU A 1 . ? 1_555 ? 2 AC1 6 OMZ A 2 ? OMZ A 2 . ? 1_555 ? 3 AC1 6 ASN A 3 ? ASN A 3 . ? 1_555 ? 4 AC1 6 GHP A 4 ? GHP A 4 . ? 1_555 ? 5 AC1 6 OMY A 6 ? OMY A 6 . ? 1_555 ? 6 AC1 6 MLU B 1 ? MLU B 1 . ? 3_545 ? 7 AC2 7 MLU B 1 ? MLU B 1 . ? 1_555 ? 8 AC2 7 OMZ B 2 ? OMZ B 2 . ? 1_555 ? 9 AC2 7 ASN B 3 ? ASN B 3 . ? 1_555 ? 10 AC2 7 GHP B 4 ? GHP B 4 . ? 1_555 ? 11 AC2 7 GHP C 4 ? GHP C 4 . ? 7_555 ? 12 AC2 7 OMY C 6 ? OMY C 6 . ? 7_555 ? 13 AC2 7 HOH N . ? HOH D 2005 . ? 4_554 ? 14 AC3 7 MLU C 1 ? MLU C 1 . ? 1_555 ? 15 AC3 7 OMZ C 2 ? OMZ C 2 . ? 1_555 ? 16 AC3 7 ASN C 3 ? ASN C 3 . ? 1_555 ? 17 AC3 7 GHP C 4 ? GHP C 4 . ? 1_555 ? 18 AC3 7 DMS H . ? DMS C 12 . ? 1_555 ? 19 AC3 7 HOH M . ? HOH C 2013 . ? 1_555 ? 20 AC3 7 3FG D 7 ? 3FG D 7 . ? 4_454 ? 21 AC4 5 GHP C 4 ? GHP C 4 . ? 1_555 ? 22 AC4 5 GHP C 5 ? GHP C 5 . ? 1_555 ? 23 AC4 5 OMY C 6 ? OMY C 6 . ? 1_555 ? 24 AC4 5 3FG C 7 ? 3FG C 7 . ? 1_555 ? 25 AC4 5 ACY G . ? ACY C 11 . ? 1_555 ? 26 AC5 6 3FG C 7 ? 3FG C 7 . ? 3_555 ? 27 AC5 6 MLU D 1 ? MLU D 1 . ? 1_555 ? 28 AC5 6 OMZ D 2 ? OMZ D 2 . ? 1_555 ? 29 AC5 6 ASN D 3 ? ASN D 3 . ? 1_555 ? 30 AC5 6 GHP D 4 ? GHP D 4 . ? 1_555 ? 31 AC5 6 HOH N . ? HOH D 2006 . ? 1_555 ? 32 AC6 5 OMZ B 2 ? OMZ B 2 . ? 5_555 ? 33 AC6 5 GHP B 4 ? GHP B 4 . ? 5_555 ? 34 AC6 5 GHP D 5 ? GHP D 5 . ? 1_555 ? 35 AC6 5 OMY D 6 ? OMY D 6 . ? 1_555 ? 36 AC6 5 3FG D 7 ? 3FG D 7 . ? 1_555 ? 37 AC7 35 ACY E . ? ACY A 11 . ? 1_555 ? 38 AC7 35 HOH K . ? HOH A 2001 . ? 1_555 ? 39 AC7 35 HOH K . ? HOH A 2005 . ? 1_555 ? 40 AC7 35 HOH K . ? HOH A 2007 . ? 1_555 ? 41 AC7 35 HOH K . ? HOH A 2008 . ? 1_555 ? 42 AC7 35 HOH K . ? HOH A 2009 . ? 1_555 ? 43 AC7 35 HOH K . ? HOH A 2011 . ? 1_555 ? 44 AC7 35 HOH K . ? HOH A 2012 . ? 1_555 ? 45 AC7 35 HOH K . ? HOH A 2013 . ? 1_555 ? 46 AC7 35 HOH K . ? HOH A 2014 . ? 1_555 ? 47 AC7 35 HOH K . ? HOH A 2015 . ? 1_555 ? 48 AC7 35 HOH K . ? HOH A 2016 . ? 1_555 ? 49 AC7 35 HOH K . ? HOH A 2017 . ? 1_555 ? 50 AC7 35 HOH K . ? HOH A 2018 . ? 5_655 ? 51 AC7 35 HOH K . ? HOH A 2018 . ? 1_555 ? 52 AC7 35 MLU B 1 ? MLU B 1 . ? 3_545 ? 53 AC7 35 OMZ B 2 ? OMZ B 2 . ? 1_555 ? 54 AC7 35 ASN B 3 ? ASN B 3 . ? 1_555 ? 55 AC7 35 GHP B 4 ? GHP B 4 . ? 1_555 ? 56 AC7 35 GHP B 5 ? GHP B 5 . ? 1_555 ? 57 AC7 35 OMY B 6 ? OMY B 6 . ? 1_555 ? 58 AC7 35 3FG B 7 ? 3FG B 7 . ? 3_645 ? 59 AC7 35 HOH L . ? HOH B 2011 . ? 1_555 ? 60 AC7 35 MLU C 1 ? MLU C 1 . ? 1_655 ? 61 AC7 35 OMZ C 2 ? OMZ C 2 . ? 1_655 ? 62 AC7 35 OMZ C 2 ? OMZ C 2 . ? 5_545 ? 63 AC7 35 ASN C 3 ? ASN C 3 . ? 1_655 ? 64 AC7 35 GHP C 5 ? GHP C 5 . ? 1_655 ? 65 AC7 35 3FG C 7 ? 3FG C 7 . ? 1_655 ? 66 AC7 35 HOH M . ? HOH C 2013 . ? 1_655 ? 67 AC7 35 MLU D 1 ? MLU D 1 . ? 4_554 ? 68 AC7 35 OMY D 6 ? OMY D 6 . ? 5_545 ? 69 AC7 35 HOH N . ? HOH D 2003 . ? 1_555 ? 70 AC7 35 HOH N . ? HOH D 2007 . ? 5_545 ? 71 AC7 35 HOH N . ? HOH D 2010 . ? 5_545 ? 72 AC8 38 MLU A 1 ? MLU A 1 . ? 4_554 ? 73 AC8 38 OMZ A 2 ? OMZ A 2 . ? 4_554 ? 74 AC8 38 ASN A 3 ? ASN A 3 . ? 1_555 ? 75 AC8 38 GHP A 4 ? GHP A 4 . ? 1_555 ? 76 AC8 38 GHP A 5 ? GHP A 5 . ? 1_555 ? 77 AC8 38 OMY A 6 ? OMY A 6 . ? 1_555 ? 78 AC8 38 3FG A 7 ? 3FG A 7 . ? 4_564 ? 79 AC8 38 ACY E . ? ACY A 11 . ? 4_554 ? 80 AC8 38 HOH K . ? HOH A 2007 . ? 7_555 ? 81 AC8 38 HOH K . ? HOH A 2013 . ? 1_555 ? 82 AC8 38 HOH K . ? HOH A 2016 . ? 4_564 ? 83 AC8 38 ACY F . ? ACY B 11 . ? 1_555 ? 84 AC8 38 HOH L . ? HOH B 2001 . ? 1_555 ? 85 AC8 38 HOH L . ? HOH B 2004 . ? 1_555 ? 86 AC8 38 HOH L . ? HOH B 2005 . ? 1_555 ? 87 AC8 38 HOH L . ? HOH B 2007 . ? 1_555 ? 88 AC8 38 HOH L . ? HOH B 2008 . ? 1_555 ? 89 AC8 38 HOH L . ? HOH B 2011 . ? 1_555 ? 90 AC8 38 HOH L . ? HOH B 2012 . ? 1_555 ? 91 AC8 38 HOH L . ? HOH B 2013 . ? 1_555 ? 92 AC8 38 HOH L . ? HOH B 2014 . ? 1_555 ? 93 AC8 38 HOH L . ? HOH B 2015 . ? 1_555 ? 94 AC8 38 MLU C 1 ? MLU C 1 . ? 1_655 ? 95 AC8 38 OMZ C 2 ? OMZ C 2 . ? 7_555 ? 96 AC8 38 GHP C 4 ? GHP C 4 . ? 7_555 ? 97 AC8 38 GHP C 5 ? GHP C 5 . ? 4_554 ? 98 AC8 38 OMY C 6 ? OMY C 6 . ? 7_555 ? 99 AC8 38 MLU D 1 ? MLU D 1 . ? 4_554 ? 100 AC8 38 OMZ D 2 ? OMZ D 2 . ? 4_554 ? 101 AC8 38 ASN D 3 ? ASN D 3 . ? 4_554 ? 102 AC8 38 GHP D 4 ? GHP D 4 . ? 7_555 ? 103 AC8 38 GHP D 5 ? GHP D 5 . ? 4_554 ? 104 AC8 38 3FG D 7 ? 3FG D 7 . ? 4_554 ? 105 AC8 38 3FG D 7 ? 3FG D 7 . ? 5_545 ? 106 AC8 38 DMS J . ? DMS D 12 . ? 5_545 ? 107 AC8 38 HOH N . ? HOH D 2003 . ? 4_554 ? 108 AC8 38 HOH N . ? HOH D 2005 . ? 4_554 ? 109 AC8 38 HOH N . ? HOH D 2006 . ? 4_554 ? 110 AC9 36 MLU A 1 ? MLU A 1 . ? 1_455 ? 111 AC9 36 ASN A 3 ? ASN A 3 . ? 1_455 ? 112 AC9 36 GHP A 4 ? GHP A 4 . ? 1_455 ? 113 AC9 36 GHP A 5 ? GHP A 5 . ? 1_455 ? 114 AC9 36 OMY A 6 ? OMY A 6 . ? 5_555 ? 115 AC9 36 3FG A 7 ? 3FG A 7 . ? 1_455 ? 116 AC9 36 MLU B 1 ? MLU B 1 . ? 7_555 ? 117 AC9 36 OMZ B 2 ? OMZ B 2 . ? 7_555 ? 118 AC9 36 GHP B 4 ? GHP B 4 . ? 7_555 ? 119 AC9 36 OMY B 6 ? OMY B 6 . ? 1_455 ? 120 AC9 36 3FG B 7 ? 3FG B 7 . ? 3_545 ? 121 AC9 36 ACY F . ? ACY B 11 . ? 7_555 ? 122 AC9 36 ACY G . ? ACY C 11 . ? 1_555 ? 123 AC9 36 DMS H . ? DMS C 12 . ? 1_555 ? 124 AC9 36 HOH M . ? HOH C 2001 . ? 1_555 ? 125 AC9 36 HOH M . ? HOH C 2002 . ? 1_555 ? 126 AC9 36 HOH M . ? HOH C 2005 . ? 1_555 ? 127 AC9 36 HOH M . ? HOH C 2007 . ? 1_555 ? 128 AC9 36 HOH M . ? HOH C 2008 . ? 1_555 ? 129 AC9 36 HOH M . ? HOH C 2010 . ? 1_555 ? 130 AC9 36 HOH M . ? HOH C 2013 . ? 1_555 ? 131 AC9 36 HOH M . ? HOH C 2014 . ? 1_555 ? 132 AC9 36 HOH M . ? HOH C 2015 . ? 1_555 ? 133 AC9 36 HOH M . ? HOH C 2016 . ? 1_555 ? 134 AC9 36 HOH M . ? HOH C 2017 . ? 1_555 ? 135 AC9 36 HOH M . ? HOH C 2018 . ? 1_555 ? 136 AC9 36 HOH M . ? HOH C 2019 . ? 1_555 ? 137 AC9 36 MLU D 1 ? MLU D 1 . ? 4_454 ? 138 AC9 36 ASN D 3 ? ASN D 3 . ? 1_555 ? 139 AC9 36 GHP D 4 ? GHP D 4 . ? 1_555 ? 140 AC9 36 GHP D 5 ? GHP D 5 . ? 1_555 ? 141 AC9 36 GHP D 5 ? GHP D 5 . ? 4_454 ? 142 AC9 36 OMY D 6 ? OMY D 6 . ? 1_555 ? 143 AC9 36 3FG D 7 ? 3FG D 7 . ? 4_454 ? 144 AC9 36 ACY I . ? ACY D 11 . ? 4_454 ? 145 AC9 36 HOH N . ? HOH D 2001 . ? 4_454 ? 146 BC1 40 GHP A 4 ? GHP A 4 . ? 5_555 ? 147 BC1 40 GHP A 5 ? GHP A 5 . ? 3_545 ? 148 BC1 40 OMY A 6 ? OMY A 6 . ? 5_555 ? 149 BC1 40 HOH K . ? HOH A 2017 . ? 1_455 ? 150 BC1 40 MLU B 1 ? MLU B 1 . ? 7_555 ? 151 BC1 40 OMZ B 2 ? OMZ B 2 . ? 5_555 ? 152 BC1 40 ASN B 3 ? ASN B 3 . ? 3_545 ? 153 BC1 40 GHP B 4 ? GHP B 4 . ? 3_545 ? 154 BC1 40 GHP B 5 ? GHP B 5 . ? 3_545 ? 155 BC1 40 3FG B 7 ? 3FG B 7 . ? 3_545 ? 156 BC1 40 HOH L . ? HOH B 2001 . ? 7_555 ? 157 BC1 40 HOH L . ? HOH B 2004 . ? 5_555 ? 158 BC1 40 HOH L . ? HOH B 2007 . ? 3_545 ? 159 BC1 40 HOH L . ? HOH B 2015 . ? 3_545 ? 160 BC1 40 MLU C 1 ? MLU C 1 . ? 3_555 ? 161 BC1 40 OMZ C 2 ? OMZ C 2 . ? 1_555 ? 162 BC1 40 OMZ C 2 ? OMZ C 2 . ? 3_555 ? 163 BC1 40 ASN C 3 ? ASN C 3 . ? 1_555 ? 164 BC1 40 GHP C 4 ? GHP C 4 . ? 1_555 ? 165 BC1 40 GHP C 5 ? GHP C 5 . ? 1_555 ? 166 BC1 40 OMY C 6 ? OMY C 6 . ? 1_555 ? 167 BC1 40 3FG C 7 ? 3FG C 7 . ? 3_555 ? 168 BC1 40 ACY G . ? ACY C 11 . ? 3_555 ? 169 BC1 40 HOH M . ? HOH C 2005 . ? 1_555 ? 170 BC1 40 HOH M . ? HOH C 2010 . ? 1_555 ? 171 BC1 40 ACY I . ? ACY D 11 . ? 1_555 ? 172 BC1 40 DMS J . ? DMS D 12 . ? 1_555 ? 173 BC1 40 HOH N . ? HOH D 2001 . ? 1_555 ? 174 BC1 40 HOH N . ? HOH D 2002 . ? 1_555 ? 175 BC1 40 HOH N . ? HOH D 2003 . ? 1_555 ? 176 BC1 40 HOH N . ? HOH D 2004 . ? 1_555 ? 177 BC1 40 HOH N . ? HOH D 2005 . ? 1_555 ? 178 BC1 40 HOH N . ? HOH D 2006 . ? 1_555 ? 179 BC1 40 HOH N . ? HOH D 2007 . ? 1_555 ? 180 BC1 40 HOH N . ? HOH D 2010 . ? 1_555 ? 181 BC1 40 HOH N . ? HOH D 2011 . ? 1_555 ? 182 BC1 40 HOH N . ? HOH D 2012 . ? 1_555 ? 183 BC1 40 HOH N . ? HOH D 2013 . ? 1_555 ? 184 BC1 40 HOH N . ? HOH D 2014 . ? 1_555 ? 185 BC1 40 HOH N . ? HOH D 2015 . ? 1_555 ? # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASN A 3 ? ? -125.45 -55.08 2 1 ASN B 3 ? ? -121.54 -59.59 3 1 ASN D 3 ? ? -106.96 -66.47 # _pdbx_molecule_features.prd_id PRD_000206 _pdbx_molecule_features.name 'VANCOMYCIN AGLYCON' _pdbx_molecule_features.type Oligopeptide _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;VANCOMYCIN AGLYCON IS THE NONSUGAR COMPONENT OF VANCOMYCIN, CONSISTING OF THE TRICYCLIC HEPTAPEPTIDE ONLY. ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000206 A 2 PRD_000206 B 3 PRD_000206 C 4 PRD_000206 D # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id C _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 2003 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id M _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_entry_details.entry_id 1GHG _pdbx_entry_details.compound_details ;VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE AND VANCOSAMINE. HERE, VANCOMYCIN AGLYCON IS REPRESENTED BY SEQUENCE (SEQRES) ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 3FG N N N N 1 3FG OD1 O N N 2 3FG CD1 C Y N 3 3FG CG1 C Y N 4 3FG CZ C Y N 5 3FG CD2 C Y N 6 3FG OD2 O N N 7 3FG CG2 C Y N 8 3FG CB C Y N 9 3FG CA C N S 10 3FG C C N N 11 3FG O O N N 12 3FG OXT O N N 13 3FG H H N N 14 3FG H2 H N N 15 3FG HA H N N 16 3FG HD1 H N N 17 3FG HG1 H N N 18 3FG HZ H N N 19 3FG HD2 H N N 20 3FG HG2 H N N 21 3FG HXT H N N 22 ACY C C N N 23 ACY O O N N 24 ACY OXT O N N 25 ACY CH3 C N N 26 ACY HXT H N N 27 ACY H1 H N N 28 ACY H2 H N N 29 ACY H3 H N N 30 ASN N N N N 31 ASN CA C N S 32 ASN C C N N 33 ASN O O N N 34 ASN CB C N N 35 ASN CG C N N 36 ASN OD1 O N N 37 ASN ND2 N N N 38 ASN OXT O N N 39 ASN H H N N 40 ASN H2 H N N 41 ASN HA H N N 42 ASN HB2 H N N 43 ASN HB3 H N N 44 ASN HD21 H N N 45 ASN HD22 H N N 46 ASN HXT H N N 47 DMS S S N N 48 DMS O O N N 49 DMS C1 C N N 50 DMS C2 C N N 51 DMS H11 H N N 52 DMS H12 H N N 53 DMS H13 H N N 54 DMS H21 H N N 55 DMS H22 H N N 56 DMS H23 H N N 57 GHP N N N N 58 GHP CA C N R 59 GHP C C N N 60 GHP O O N N 61 GHP OXT O N N 62 GHP C1 C Y N 63 GHP C2 C Y N 64 GHP C3 C Y N 65 GHP C4 C Y N 66 GHP O4 O N N 67 GHP C5 C Y N 68 GHP C6 C Y N 69 GHP H H N N 70 GHP H2 H N N 71 GHP HA H N N 72 GHP HXT H N N 73 GHP HC2 H N N 74 GHP H3 H N N 75 GHP HO4 H N N 76 GHP H5 H N N 77 GHP H6 H N N 78 HOH O O N N 79 HOH H1 H N N 80 HOH H2 H N N 81 MLU N N N N 82 MLU CN C N N 83 MLU CA C N R 84 MLU C C N N 85 MLU O O N N 86 MLU CB C N N 87 MLU CG C N N 88 MLU CD1 C N N 89 MLU CD2 C N N 90 MLU OXT O N N 91 MLU H H N N 92 MLU HCN1 H N N 93 MLU HCN2 H N N 94 MLU HCN3 H N N 95 MLU HA H N N 96 MLU HB2 H N N 97 MLU HB3 H N N 98 MLU HXT H N N 99 MLU HG H N N 100 MLU HD11 H N N 101 MLU HD12 H N N 102 MLU HD13 H N N 103 MLU HD21 H N N 104 MLU HD22 H N N 105 MLU HD23 H N N 106 OMY N N N N 107 OMY CA C N S 108 OMY OCZ O N N 109 OMY CE2 C Y N 110 OMY CE1 C Y N 111 OMY CZ C Y N 112 OMY CG C Y N 113 OMY CD2 C Y N 114 OMY CD1 C Y N 115 OMY CB C N R 116 OMY CL CL N N 117 OMY O O N N 118 OMY C C N N 119 OMY ODE O N N 120 OMY OXT O N N 121 OMY H H N N 122 OMY H2 H N N 123 OMY HA H N N 124 OMY HCZ H N N 125 OMY HE2 H N N 126 OMY HD2 H N N 127 OMY HD1 H N N 128 OMY HB H N N 129 OMY HXT H N N 130 OMY HDE H N N 131 OMZ N N N N 132 OMZ CA C N R 133 OMZ C C N N 134 OMZ O O N N 135 OMZ OXT O N N 136 OMZ CB C N R 137 OMZ OC O N N 138 OMZ CG C Y N 139 OMZ CD1 C Y N 140 OMZ CD2 C Y N 141 OMZ CE1 C Y N 142 OMZ CL CL N N 143 OMZ CE2 C Y N 144 OMZ CZ C Y N 145 OMZ OH O N N 146 OMZ H H N N 147 OMZ H2 H N N 148 OMZ HA H N N 149 OMZ HB H N N 150 OMZ HXT H N N 151 OMZ HC H N N 152 OMZ HD1 H N N 153 OMZ HD2 H N N 154 OMZ HE2 H N N 155 OMZ HH H N N 156 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 3FG N CA sing N N 1 3FG OD1 CD1 sing N N 2 3FG CD1 CG1 sing Y N 3 3FG CD1 CZ doub Y N 4 3FG CG1 CB doub Y N 5 3FG CZ CD2 sing Y N 6 3FG CD2 OD2 sing N N 7 3FG CD2 CG2 doub Y N 8 3FG CG2 CB sing Y N 9 3FG CB CA sing N N 10 3FG CA C sing N N 11 3FG C O doub N N 12 3FG C OXT sing N N 13 3FG N H sing N N 14 3FG N H2 sing N N 15 3FG CA HA sing N N 16 3FG OD1 HD1 sing N N 17 3FG CG1 HG1 sing N N 18 3FG CZ HZ sing N N 19 3FG OD2 HD2 sing N N 20 3FG CG2 HG2 sing N N 21 3FG OXT HXT sing N N 22 ACY C O doub N N 23 ACY C OXT sing N N 24 ACY C CH3 sing N N 25 ACY OXT HXT sing N N 26 ACY CH3 H1 sing N N 27 ACY CH3 H2 sing N N 28 ACY CH3 H3 sing N N 29 ASN N CA sing N N 30 ASN N H sing N N 31 ASN N H2 sing N N 32 ASN CA C sing N N 33 ASN CA CB sing N N 34 ASN CA HA sing N N 35 ASN C O doub N N 36 ASN C OXT sing N N 37 ASN CB CG sing N N 38 ASN CB HB2 sing N N 39 ASN CB HB3 sing N N 40 ASN CG OD1 doub N N 41 ASN CG ND2 sing N N 42 ASN ND2 HD21 sing N N 43 ASN ND2 HD22 sing N N 44 ASN OXT HXT sing N N 45 DMS S O doub N N 46 DMS S C1 sing N N 47 DMS S C2 sing N N 48 DMS C1 H11 sing N N 49 DMS C1 H12 sing N N 50 DMS C1 H13 sing N N 51 DMS C2 H21 sing N N 52 DMS C2 H22 sing N N 53 DMS C2 H23 sing N N 54 GHP N CA sing N N 55 GHP N H sing N N 56 GHP N H2 sing N N 57 GHP CA C sing N N 58 GHP CA C1 sing N N 59 GHP CA HA sing N N 60 GHP C O doub N N 61 GHP C OXT sing N N 62 GHP OXT HXT sing N N 63 GHP C1 C2 doub Y N 64 GHP C1 C6 sing Y N 65 GHP C2 C3 sing Y N 66 GHP C2 HC2 sing N N 67 GHP C3 C4 doub Y N 68 GHP C3 H3 sing N N 69 GHP C4 O4 sing N N 70 GHP C4 C5 sing Y N 71 GHP O4 HO4 sing N N 72 GHP C5 C6 doub Y N 73 GHP C5 H5 sing N N 74 GHP C6 H6 sing N N 75 HOH O H1 sing N N 76 HOH O H2 sing N N 77 MLU N CN sing N N 78 MLU N CA sing N N 79 MLU CA C sing N N 80 MLU CA CB sing N N 81 MLU C O doub N N 82 MLU C OXT sing N N 83 MLU CB CG sing N N 84 MLU CG CD1 sing N N 85 MLU CG CD2 sing N N 86 MLU N H sing N N 87 MLU CN HCN1 sing N N 88 MLU CN HCN2 sing N N 89 MLU CN HCN3 sing N N 90 MLU CA HA sing N N 91 MLU CB HB2 sing N N 92 MLU CB HB3 sing N N 93 MLU OXT HXT sing N N 94 MLU CG HG sing N N 95 MLU CD1 HD11 sing N N 96 MLU CD1 HD12 sing N N 97 MLU CD1 HD13 sing N N 98 MLU CD2 HD21 sing N N 99 MLU CD2 HD22 sing N N 100 MLU CD2 HD23 sing N N 101 OMY N CA sing N N 102 OMY OCZ CZ sing N N 103 OMY CZ CE2 sing Y N 104 OMY CZ CE1 doub Y N 105 OMY CE2 CD2 doub Y N 106 OMY CD2 CG sing Y N 107 OMY CG CD1 doub Y N 108 OMY CG CB sing N N 109 OMY CD1 CE1 sing Y N 110 OMY CE1 CL sing N N 111 OMY C O doub N N 112 OMY C CA sing N N 113 OMY C OXT sing N N 114 OMY CA CB sing N N 115 OMY CB ODE sing N N 116 OMY N H sing N N 117 OMY N H2 sing N N 118 OMY CA HA sing N N 119 OMY OCZ HCZ sing N N 120 OMY CE2 HE2 sing N N 121 OMY CD2 HD2 sing N N 122 OMY CD1 HD1 sing N N 123 OMY CB HB sing N N 124 OMY OXT HXT sing N N 125 OMY ODE HDE sing N N 126 OMZ N CA sing N N 127 OMZ CA C sing N N 128 OMZ CA CB sing N N 129 OMZ C O doub N N 130 OMZ C OXT sing N N 131 OMZ CL CE1 sing N N 132 OMZ CB OC sing N N 133 OMZ CB CG sing N N 134 OMZ CG CD1 doub Y N 135 OMZ CG CD2 sing Y N 136 OMZ CD1 CE1 sing Y N 137 OMZ CD2 CE2 doub Y N 138 OMZ CE1 CZ doub Y N 139 OMZ CE2 CZ sing Y N 140 OMZ CZ OH sing N N 141 OMZ N H sing N N 142 OMZ N H2 sing N N 143 OMZ CA HA sing N N 144 OMZ CB HB sing N N 145 OMZ OXT HXT sing N N 146 OMZ OC HC sing N N 147 OMZ CD1 HD1 sing N N 148 OMZ CD2 HD2 sing N N 149 OMZ CE2 HE2 sing N N 150 OMZ OH HH sing N N 151 # _atom_sites.entry_id 1GHG _atom_sites.fract_transf_matrix[1][1] 0.033921 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033921 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.013464 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CL N O S # loop_