0.035211 0.000000 0.000000 0.000000 0.035211 0.000000 0.000000 0.000000 0.015214 0.00000 0.00000 0.00000 Loll, P.J. Kaplan, J. Selinsky, B. Axelsen, P.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 28.400 28.400 65.730 C8 H9 N O4 183.161 (2S)-amino(3,5-dihydroxyphenyl)ethanoic acid L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C6 H12 O6 180.156 beta-D-glucopyranose beta-D-glucose; D-glucose; glucose D-saccharide, beta linking Cl -1 35.453 CHLORIDE ION non-polymer C8 H9 N O3 167.162 (2R)-amino(4-hydroxyphenyl)ethanoic acid D-peptide linking H2 O 18.015 WATER non-polymer C3 H6 O3 90.078 LACTIC ACID non-polymer C7 H15 N O2 145.199 N-methyl-D-leucine D-peptide linking C9 H10 Cl N O4 231.633 n (betaR)-3-chloro-beta-hydroxy-L-tyrosine L-peptide linking C9 H10 Cl N O4 231.633 (betaR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE D-peptide linking C7 H15 N O3 161.199 vancosamine (1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose L-saccharide, alpha linking N 1 N N N 2 N O Y 3 N C Y 4 N C Y 5 N C Y 6 N C N 7 N O Y 8 N C Y 9 N C N 10 S C N 11 N C N 12 N O N 13 N O N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N N N 24 S C N 25 N C N 26 N O N 27 N C N 28 N C N 29 N O N 30 N N N 31 N O N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 R C N 41 S C N 42 S C N 43 R C N 44 N C N 45 R C N 46 N O N 47 N O N 48 N O N 49 N O N 50 N O N 51 N O N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N CL N 65 N N N 66 R C N 67 N C N 68 N O N 69 N O Y 70 N C Y 71 N C Y 72 N C Y 73 N C N 74 N O Y 75 N C Y 76 N C N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N O N 87 N H N 88 N H N 89 N C N 90 R C N 91 N C N 92 N O N 93 N O N 94 N O N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N N N 102 N C N 103 R C N 104 N C N 105 N O N 106 N C N 107 N C N 108 N C N 109 N C N 110 N O N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N N N 127 S C N 128 N O Y 129 N C Y 130 N C Y 131 N C Y 132 N C Y 133 N C Y 134 N C N 135 R C N 136 N CL N 137 N O N 138 N C N 139 N O N 140 N O N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N N N 152 R C N 153 N C N 154 N O N 155 N O N 156 R C N 157 N O Y 158 N C Y 159 N C Y 160 N C Y 161 N C N 162 N CL Y 163 N C Y 164 N C N 165 N O N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 R C N 177 N C N 178 S C N 179 N N N 180 N C N 181 S C N 182 N O N 183 S C N 184 N O N 185 N C N 186 N O N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 1 N sing N 2 N sing Y 3 N sing Y 4 N doub Y 5 N doub Y 6 N sing N 7 N sing Y 8 N doub Y 9 N sing N 10 N sing N 11 N sing N 12 N doub N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N doub N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N doub N 70 N sing N 71 N sing Y 72 N doub Y 73 N sing Y 74 N sing N 75 N sing Y 76 N doub N 77 N sing N 78 N sing Y 79 N sing N 80 N sing Y 81 N doub N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N doub N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N doub N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing Y 123 N sing Y 124 N doub Y 125 N doub Y 126 N sing Y 127 N doub N 128 N sing Y 129 N sing N 130 N sing N 131 N doub N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N doub N 150 N sing N 151 N sing N 152 N sing N 153 N sing Y 154 N doub Y 155 N sing Y 156 N sing Y 157 N doub Y 158 N doub Y 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing US J.Med.Chem. JMCMAR 0151 0022-2623 42 4714 4719 10.1021/jm990361t 10579833 Vancomycin binding to low-affinity ligands: delineating a minimum set of interactions necessary for high-affinity binding. 1999 10.2210/pdb1c0q/pdb pdb_00001c0q 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 IMAGE PLATE 1997-05-05 MAR scanner 300 mm plate SINGLE WAVELENGTH M x-ray 1 0.978 1.0 X12B NSLS 0.978 SYNCHROTRON NSLS BEAMLINE X12B 1149.977 VANCOMYCIN 2 syn polymer 323.340 vancosamine-(1-2)-beta-D-glucopyranose 2 man branched 35.453 CHLORIDE ION 3 syn non-polymer 90.078 LACTIC ACID 1 syn non-polymer 18.015 water 46 nat water no yes (MLU)(OMZ)N(GHP)(GHP)(OMY)(3FG) XXNGGYX A,B polypeptide(L) n n n n n n n 1 2.88 57.31 VAPOR DIFFUSION, HANGING DROP 4.6 Sodium chloride, 2-acetoxy-D-propanoic acid, pH 4.6, vapor diffusion/hanging drop, temperature 291K 291 atom_site chem_comp entity entity_poly pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_molecule pdbx_nonpoly_scheme pdbx_struct_assembly_gen pdbx_struct_special_symmetry pdbx_validate_close_contact software struct_asym struct_conn struct_site struct_site_gen atom_site chem_comp chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Carbohydrate remediation repository Remediation Version format compliance Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Other Structure summary Derived calculations Advisory Atomic model Data collection Derived calculations Polymer sequence Refinement description Structure summary Atomic model Data collection Database references Derived calculations Structure summary 1 0 1999-07-30 1 1 2008-04-26 1 2 2011-07-13 1 3 2011-07-27 1 4 2012-12-12 1 5 2013-03-27 1 6 2013-04-10 2 0 2020-07-29 3 0 2023-11-15 _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_alt_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.occupancy _atom_site.type_symbol _chem_comp.name _chem_comp.type _entity_poly.pdbx_seq_one_letter_code_can _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_special_symmetry.label_asym_id _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.auth_seq_id_2 _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_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.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _atom_site.auth_atom_id _atom_site.label_atom_id _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag A BGC 8 n C BGC 1 A RER 9 n C RER 2 B BGC 8 n D BGC 1 B RER 9 n D RER 2 DGlcpb b-D-glucopyranose b-D-Glcp Glc CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH ACETATE CRYSTAL STRUCTURE OF VANCOMYCIN WITH D-LACTIC ACID CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH DI-ACETYL-LYS-D-ALA-D-ALA SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXD WITH TDP AND DESVANCOSAMINYL VANCOMYCIN CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXED WITH TDP AND VANCOMYCIN CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL GLYCIN CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEXED WITH TDP AND DESVANCOSAMINYL VANCOMYCIN. CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH ACETATE RCSB Y RCSB 1999-07-20 REL oligosaccharide WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad621m-1a_1-5_3*C_3*N]/1-2/a2-b1 2 PDB2Glycan 1.1.0 WURCS [][D-1-deoxy-Glcp]{[(2+1)][a-L-2-deoxy-Fucp3N]{}} 2 PDB-CARE LINUCS C1 O2 RER BGC 2 1 2 O1 HO2 sing n n CL CHLORIDE ION LAC LACTIC ACID HOH water 31958 NOCARDIA ORIENTALIS AMYCOLATOPSIS ORIENTALIS sample 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 IS REPRESENTED BY GROUPING TOUGHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER. Antibiotic VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. VANCOMYCIN Glycopeptide CL 21 3 CL CL 21 A CL 20 3 CL CL 20 B CL 20 3 CL CL 10 B LAC 23 4 LAC LAC 23 B HOH 2001 5 HOH HOH 2001 A HOH 2002 5 HOH HOH 2002 A HOH 2003 5 HOH HOH 2003 A HOH 2004 5 HOH HOH 2004 A HOH 2005 5 HOH HOH 2005 A HOH 2006 5 HOH HOH 2006 A HOH 2007 5 HOH HOH 2007 A HOH 2008 5 HOH HOH 2008 A HOH 2009 5 HOH HOH 2009 A HOH 2004 5 HOH HOH 2010 A HOH 2011 5 HOH HOH 2011 A HOH 2012 5 HOH HOH 2012 A HOH 2013 5 HOH HOH 2013 A HOH 2014 5 HOH HOH 2014 A HOH 2015 5 HOH HOH 2015 A HOH 2016 5 HOH HOH 2016 A HOH 2017 5 HOH HOH 2017 A HOH 2018 5 HOH HOH 2018 A HOH 2019 5 HOH HOH 2019 A HOH 2020 5 HOH HOH 2020 A HOH 2021 5 HOH HOH 2021 A HOH 2022 5 HOH HOH 2022 A HOH 2023 5 HOH HOH 2023 A HOH 2024 5 HOH HOH 2024 A HOH 2025 5 HOH HOH 2025 A HOH 2026 5 HOH HOH 2026 A HOH 2027 5 HOH HOH 2027 A HOH 2028 5 HOH HOH 2028 A HOH 2029 5 HOH HOH 2029 A HOH 2015 5 HOH HOH 2030 A HOH 2016 5 HOH HOH 2031 A HOH 2001 5 HOH HOH 2001 B HOH 2002 5 HOH HOH 2002 B HOH 2003 5 HOH HOH 2003 B HOH 2005 5 HOH HOH 2005 B HOH 2006 5 HOH HOH 2006 B HOH 2007 5 HOH HOH 2007 B HOH 2008 5 HOH HOH 2008 B HOH 2009 5 HOH HOH 2009 B HOH 2010 5 HOH HOH 2010 B HOH 2011 5 HOH HOH 2011 B HOH 2012 5 HOH HOH 2012 B HOH 2013 5 HOH HOH 2013 B HOH 2014 5 HOH HOH 2014 B HOH 2010 5 HOH HOH 2015 B HOH 2017 5 HOH HOH 2017 B MLU 1 n 1 MLU 1 A OMZ 2 n 2 OMZ 2 A ASN 3 n 3 ASN 3 A GHP 4 n 4 GHP 4 A GHP 5 n 5 GHP 5 A OMY 6 n 6 OMY 6 A 3FG 7 n 7 3FG 7 A MLU 1 n 1 MLU 1 B OMZ 2 n 2 OMZ 2 B ASN 3 n 3 ASN 3 B GHP 4 n 4 GHP 4 B GHP 5 n 5 GHP 5 B OMY 6 n 6 OMY 6 B 3FG 7 n 7 3FG 7 B 0.119 0.139 1002 author_defined_assembly 2 dimeric software_defined_assembly PISA 2 dimeric 1060 -19 2540 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 6_555 x+1/2,-y+1/2,-z+1/4 crystal symmetry operation 14.2000000000 14.2000000000 16.4325000000 1 A HOH 2012 I HOH 1 D D O2 O5 BGC RER 1 2 2.16 B 1 A ASN 3 -99.63 -68.39 Refinement was carried out against F-squared using SHELXL-93. Molecular geometry and atomic displacement parameters were restrained throughout. Independent vancomycin monomers were restrained to have similar 1-2 and 1-3 distances; restraints were also imposed to limit deviations from planarity in rings and sp2 systems. Along-bond components of anisotropic displacement parameters were subjected to restraints. Solvent water atoms were restrained to be approximately isotropic and were made subject to anti-bumping restraints. Conjugate gradient refinement was used throughout, except at the last stages, when blocked least squares was used. 0.139 0.119 0.119 1.00 20.00 1002 15091 13845 92.0 RANDOM 1 THROUGHOUT ENGH & HUBER 1.00 20.00 46 257 51 0 160 0.019 1.000 20.000 1C0Q 15091 13845 2.000 0.05400 1 34.7000 11.800 92.0 0.05500 1.00 1.04 1 2.40 65.0 refinement SHELXL data reduction DENZO data scaling SCALEPACK COMPLEX OF VANCOMYCIN WITH 2-ACETOXY-D-PROPANOIC ACID 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N 3 N N 4 N N 5 N N 5 N N covale 1.348 both A MLU 1 A C MLU 1 1_555 A OMZ 2 A N OMZ 2 1_555 covale 1.347 both A OMZ 2 A C OMZ 2 1_555 A ASN 3 A N ASN 3 1_555 covale 1.395 none A OMZ 2 A OH OMZ 2 1_555 A GHP 4 A C5 GHP 4 1_555 covale 1.337 both A ASN 3 A C ASN 3 1_555 A GHP 4 A N GHP 4 1_555 covale 1.347 both A GHP 4 A C GHP 4 1_555 A GHP 5 A N GHP 5 1_555 covale 1.393 none A GHP 4 A C3 GHP 4 1_555 A OMY 6 A OCZ OMY 6 1_555 covale 1.432 one A GHP 4 A O4 GHP 4 1_555 C BGC 1 C C1 BGC 1_555 covale 1.329 both A GHP 5 A C GHP 5 1_555 A OMY 6 A N OMY 6 1_555 covale 1.508 one A GHP 5 A C3 GHP 5 1_555 A 3FG 7 A CG1 3FG 7 1_555 covale 1.321 both A OMY 6 A C OMY 6 1_555 A 3FG 7 A N 3FG 7 1_555 covale 1.344 both B MLU 1 B C MLU 1 1_555 B OMZ 2 B N OMZ 2 1_555 covale 1.340 both B OMZ 2 B C OMZ 2 1_555 B ASN 3 B N ASN 3 1_555 covale 1.398 none B OMZ 2 B OH OMZ 2 1_555 B GHP 4 B C5 GHP 4 1_555 covale 1.337 both B ASN 3 B C ASN 3 1_555 B GHP 4 B N GHP 4 1_555 covale 1.340 both B GHP 4 B C GHP 4 1_555 B GHP 5 B N GHP 5 1_555 covale 1.400 none B GHP 4 B C3 GHP 4 1_555 B OMY 6 B OCZ OMY 6 1_555 covale 1.460 one B B B GHP 4 B O4 GHP 4 1_555 D BGC 1 D C1 BGC 1_555 covale 1.460 one A A B GHP 4 B O4 GHP 4 1_555 D BGC 1 D C1 BGC 1_555 covale 1.337 both B GHP 5 B C GHP 5 1_555 B OMY 6 B N OMY 6 1_555 covale 1.497 one B GHP 5 B C3 GHP 5 1_555 B 3FG 7 B CG1 3FG 7 1_555 covale 1.326 both B OMY 6 B C OMY 6 1_555 B 3FG 7 B N 3FG 7 1_555 covale 1.579 both C BGC 1 C O2 BGC 1_555 C RER 2 C C1 RER 1_555 covale 1.264 both B D BGC 1 D O2 BGC 1_555 D RER 2 D C1 RER 1_555 covale 1.608 both A D BGC 1 D O2 BGC 1_555 D RER 2 D C1 RER 1_555 ANTIBIOTIC ANTIBIOTIC, GLYCOPEPTIDE ANTIBIOTIC A GHP 5 A GHP 5 1 A OMY 6 A OMY 6 7.26 B GHP 5 B GHP 5 1 B OMY 6 B OMY 6 20.37 NOR00681 NOR 1 NOR00681 1 7 1C0Q 1 7 NOR00681 A 1 1 7 1 7 1C0Q 1 7 NOR00681 B 1 1 7 96 P 43 21 2