0.035149 0.000000 0.000000 0.000000 0.035149 0.000000 0.000000 0.000000 0.015188 0.00000 0.00000 0.00000 Loll, P.J. Bevivino, A.E. Korty, B.D. Axelsen, P.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 28.450 28.450 65.840 C8 H9 N O4 183.161 (2S)-amino(3,5-dihydroxyphenyl)ethanoic acid L-peptide linking C2 H4 O2 60.052 ACETIC ACID non-polymer 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 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 C N 24 N O N 25 N O N 26 N C N 27 N H N 28 N H N 29 N H N 30 N H N 31 N N N 32 S C N 33 N C N 34 N O N 35 N C N 36 N C N 37 N O N 38 N N N 39 N O N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 R C N 49 S C N 50 S C N 51 R C N 52 N C N 53 R C N 54 N O N 55 N O N 56 N O N 57 N O N 58 N O N 59 N O N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N CL N 73 N N N 74 R C N 75 N C N 76 N O N 77 N O Y 78 N C Y 79 N C Y 80 N C Y 81 N C N 82 N O Y 83 N C Y 84 N C N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N O N 95 N H N 96 N H N 97 N N N 98 N C N 99 R C N 100 N C N 101 N O N 102 N C N 103 N C N 104 N C N 105 N C N 106 N O N 107 N H N 108 N H N 109 N H N 110 N H 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 N N 123 S C N 124 N O Y 125 N C Y 126 N C Y 127 N C Y 128 N C Y 129 N C Y 130 N C N 131 R C N 132 N CL N 133 N O N 134 N C N 135 N O N 136 N O N 137 N H N 138 N H N 139 N H N 140 N H 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 N N 148 R C N 149 N C N 150 N O N 151 N O N 152 R C N 153 N O Y 154 N C Y 155 N C Y 156 N C Y 157 N C N 158 N CL Y 159 N C Y 160 N C N 161 N O N 162 N H N 163 N H N 164 N H N 165 N H 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 R C N 173 N C N 174 S C N 175 N N N 176 N C N 177 S C N 178 N O N 179 S C N 180 N O N 181 N C N 182 N O N 183 N H N 184 N H N 185 N H N 186 N H 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 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 doub N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N doub N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N doub 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 sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing Y 79 N doub Y 80 N sing Y 81 N sing N 82 N sing Y 83 N doub N 84 N sing N 85 N sing Y 86 N sing N 87 N sing Y 88 N doub 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 doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing 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 Y 119 N sing Y 120 N doub Y 121 N doub Y 122 N sing Y 123 N doub N 124 N sing Y 125 N sing N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing N 131 N sing 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 doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing Y 150 N doub Y 151 N sing Y 152 N sing Y 153 N doub Y 154 N doub Y 155 N sing N 156 N sing N 157 N sing N 158 N sing N 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 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 119 1516 10.1021/JA963566P Simultaneous Recognition of a Carboxylate-Containing Ligand and an Intramolecular Surrogate Ligand in the Crystal Structure of an Asymmetric Vancomycin Dimer. 1997 10.2210/pdb1aa5/pdb pdb_00001aa5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 98 1 CCD 1996-04 ADSC M x-ray 1 0.85 1.0 X8C NSLS 0.85 SYNCHROTRON NSLS BEAMLINE X8C 1149.977 VANCOMYCIN 2 syn polymer 323.340 vancosamine-(1-2)-beta-D-glucopyranose 2 man branched 60.052 ACETIC ACID 1 syn non-polymer 35.453 CHLORIDE ION 4 syn non-polymer 18.015 water 55 nat water no yes (MLU)(OMZ)N(GHP)(GHP)(OMY)(3FG) XXNGGYX A,B polypeptide(L) n n n n n n n 2 2.90 57.53 4.6 CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF A 25 MG/ML VANCOMYCIN SOLUTION AND 2.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.6 (RESERVOIR BUFFER) AND THEN SUSPENDING THIS DROP OVER THE RESERVOIR. CRYSTALS WERE GROWN AT 293 K., VAPOR DIFFUSION - HANGING DROP atom_site chem_comp entity entity_poly pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_database_status 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 pdbx_struct_assembly_gen pdbx_struct_special_symmetry pdbx_validate_close_contact 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 Other Advisory Atomic model Data collection Derived calculations Other Polymer sequence Structure summary Atomic model Data collection Database references Derived calculations Structure summary 1 0 1997-08-20 1 1 2011-06-14 1 2 2011-07-13 1 3 2011-07-27 1 4 2012-12-12 1 5 2016-10-19 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_database_status.process_site _pdbx_struct_assembly.method_details _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 2-ACETOXY-D-PROPANOIC ACID 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 Y BNL 1997-01-23 REL 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 ACY ACETIC ACID CL CHLORIDE ION HOH water 31958 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 TOGETHER 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 ACY 11 3 ACY ACY 11 A CL 21 4 CL CL 21 A CL 22 4 CL CL 22 A CL 21 4 CL CL 21 B CL 22 4 CL CL 22 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 2010 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 2030 5 HOH HOH 2030 A HOH 2031 5 HOH HOH 2031 A HOH 2032 5 HOH HOH 2032 A HOH 2033 5 HOH HOH 2033 A HOH 2034 5 HOH HOH 2034 A HOH 2001 5 HOH HOH 2001 B HOH 2002 5 HOH HOH 2002 B HOH 2003 5 HOH HOH 2003 B HOH 2004 5 HOH HOH 2004 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 2015 5 HOH HOH 2015 B HOH 2016 5 HOH HOH 2016 B HOH 2017 5 HOH HOH 2017 B HOH 2018 5 HOH HOH 2018 B HOH 2019 5 HOH HOH 2019 B HOH 2020 5 HOH HOH 2020 B HOH 2021 5 HOH HOH 2021 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 0.112 0.124 0.112 0.124 17479 software_defined_assembly PISA 2 dimeric 1370 -32.8 2890 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 0.0000000000 -1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_554 -y+1/2,x+1/2,z-1/4 crystal symmetry operation 14.2250000000 14.2250000000 -16.4600000000 1 A HOH 2015 J HOH 1 D D O2 O5 BGC RER 1 2 2.01 B 1 D D C2 C1 BGC RER 1 2 2.18 B 1 A ASN 3 -100.65 -69.08 REFINEMENT WAS CARRIED OUT VS. F**2; SIMILAR 1,2 AND 1,3 DISTANCE RESTRAINTS WERE APPLIED TO THE TWO VANCOMYCIN MOLECULES. ALSO, RESTRAINTS WERE IMPOSED TO LIMIT DEVIATIONS OF RINGS AND PEPTIDE BONDS FROM PLANARITY AND DIFFERENCES IN ALONG-BOND COMPONENTS OF ADPS. ADPS FOR SOLVENT WERE RESTRAINED TO BE APPROXIMATELY ISOTROPIC, AND ANTIBUMPING RESTRAINTS WERE USED TO PREVENT SOLVENT WATER MOLECULES FROM VIOLATING MINIMUM CONTACT DISTANCES. CONJUGATE GRADIENT LEAST SQUARES WAS USED FOR MOST OF THE REFINEMENT, WITH BLOCKED LEAST SQUARES AT THE END. 0.124 0.124 0.89 4.00 2553 17899 3647 80.0 1 0.000 DIRECT METHODS 3 158.00 255.40 0.89 4.00 55 265 50 0 160 0.019 0.008 0.011 0.025 0.890 10.000 1AA5 17899 2.000 0.07600 1 100.0000 12.800 85.8 0.89 0.95 31.500 0.14300 1 5.60 69.3 model building SHELXL-93 refinement SHELXL-93 data reduction MADNES data reduction PROCOR data scaling XSCALE phasing SHELXL-93 VANCOMYCIN 1 N N 1 N N 2 N N 2 N N 3 N N 4 N N 4 N N 4 N N 4 N N 5 N N 5 N N covale 1.352 both A MLU 1 A C MLU 1 1_555 A OMZ 2 A N OMZ 2 1_555 covale 1.329 both A OMZ 2 A C OMZ 2 1_555 A ASN 3 A N ASN 3 1_555 covale 1.389 none A OMZ 2 A OH OMZ 2 1_555 A GHP 4 A C5 GHP 4 1_555 covale 1.319 both A ASN 3 A C ASN 3 1_555 A GHP 4 A N GHP 4 1_555 covale 1.355 both A GHP 4 A C GHP 4 1_555 A GHP 5 A N GHP 5 1_555 covale 1.394 none A GHP 4 A C3 GHP 4 1_555 A OMY 6 A OCZ OMY 6 1_555 covale 1.414 one A GHP 4 A O4 GHP 4 1_555 C BGC 1 C C1 BGC 1_555 covale 1.333 both A GHP 5 A C GHP 5 1_555 A OMY 6 A N OMY 6 1_555 covale 1.499 one A GHP 5 A C3 GHP 5 1_555 A 3FG 7 A CG1 3FG 7 1_555 covale 1.337 both A OMY 6 A C OMY 6 1_555 A 3FG 7 A N 3FG 7 1_555 covale 1.327 both B MLU 1 B C MLU 1 1_555 B OMZ 2 B N OMZ 2 1_555 covale 1.316 both B OMZ 2 B C OMZ 2 1_555 B ASN 3 B N ASN 3 1_555 covale 1.395 none B OMZ 2 B OH OMZ 2 1_555 B GHP 4 B C5 GHP 4 1_555 covale 1.341 both B ASN 3 B C ASN 3 1_555 B GHP 4 B N GHP 4 1_555 covale 1.341 both B GHP 4 B C GHP 4 1_555 B GHP 5 B N GHP 5 1_555 covale 1.383 none B GHP 4 B C3 GHP 4 1_555 B OMY 6 B OCZ OMY 6 1_555 covale 1.446 one B B B GHP 4 B O4 GHP 4 1_555 D BGC 1 D C1 BGC 1_555 covale 1.414 one A A B GHP 4 B O4 GHP 4 1_555 D BGC 1 D C1 BGC 1_555 covale 1.338 both B GHP 5 B C GHP 5 1_555 B OMY 6 B N OMY 6 1_555 covale 1.505 one B GHP 5 B C3 GHP 5 1_555 B 3FG 7 B CG1 3FG 7 1_555 covale 1.321 both B OMY 6 B C OMY 6 1_555 B 3FG 7 B N 3FG 7 1_555 covale 1.406 both C BGC 1 C O2 BGC 1_555 C RER 2 C C1 RER 1_555 covale 1.099 both B D BGC 1 D O2 BGC 1_555 D RER 2 D C1 RER 1_555 covale 1.466 both A D BGC 1 D O2 BGC 1_555 D RER 2 D C1 RER 1_555 ANTIBIOTIC GLYCOPEPTIDE, ANTIBIOTIC A GHP 5 A GHP 5 1 A OMY 6 A OMY 6 6.04 B GHP 5 B GHP 5 1 B OMY 6 B OMY 6 18.86 NOR00681 NOR 1 NOR00681 1 7 1AA5 1 7 NOR00681 A 1 1 7 1 7 1AA5 1 7 NOR00681 B 1 1 7 96 P 43 21 2