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(-) Description

Title :  COMPLEX OF VANCOMYCIN WITH 2-ACETOXY-D-PROPANOIC ACID
 
Authors :  P. J. Loll, J. Kaplan, B. Selinsky, P. H. Axelsen
Date :  20 Jul 99  (Deposition) - 30 Jul 99  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Antibiotic, Glycopeptide Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Loll, J. Kaplan, B. S. Selinsky, P. H. Axelsen
Vancomycin Binding To Low-Affinity Ligands: Delineating A Minimum Set Of Interactions Necessary For High-Affinity Binding.
J. Med. Chem. V. 42 4714 1999
PubMed-ID: 10579833  |  Reference-DOI: 10.1021/JM990361T

(-) Compounds

Molecule 1 - VANCOMYCIN
    Chains: A, B
    Engineered: YES
    Organism Common: NOCARDIA ORIENTALIS
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 20)

Asymmetric Unit (9, 20)
No.NameCountTypeFull Name
13FG2Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC2Ligand/IonBETA-D-GLUCOSE
3CL3Ligand/IonCHLORIDE ION
4GHP4Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
5LAC1Ligand/IonLACTIC ACID
6MLU2Mod. Amino AcidN-METHYL-D-LEUCINE
7OMY2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RER2Ligand/Ion(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
Biological Unit 1 (8, 17)
No.NameCountTypeFull Name
13FG2Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC2Ligand/IonBETA-D-GLUCOSE
3CL-1Ligand/IonCHLORIDE ION
4GHP4Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
5LAC1Ligand/IonLACTIC ACID
6MLU2Mod. Amino AcidN-METHYL-D-LEUCINE
7OMY2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RER2Ligand/Ion(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
Biological Unit 2 (7, 8)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3CL-1Ligand/IonCHLORIDE ION
4GHP2Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
5LAC-1Ligand/IonLACTIC ACID
6MLU1Mod. Amino AcidN-METHYL-D-LEUCINE
7OMY1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RER1Ligand/Ion(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECL A:21 , HOH A:2001 , HOH A:2002 , HOH A:2007 , HOH A:2008 , HOH A:2012 , HOH A:2013 , HOH A:2014 , HOH A:2015 , HOH A:2016 , HOH A:2017 , HOH A:2018 , HOH A:2019 , HOH A:2020 , HOH A:2021 , HOH A:2022 , HOH A:2025 , HOH A:2026 , HOH A:2027 , HOH A:2029 , MLU B:1 , OMZ B:2 , ASN B:3 , GHP B:4 , GHP B:5 , OMY B:6 , 3FG B:7 , BGC B:8 , RER B:9 , CL B:20 , HOH B:2001 , HOH B:2011BINDING SITE FOR CHAIN A OF VANCOMYCIN
2AC2SOFTWAREMLU A:1 , OMZ A:2 , ASN A:3 , GHP A:4 , GHP A:5 , OMY A:6 , 3FG A:7 , BGC A:8 , RER A:9 , CL A:21 , HOH A:2002 , HOH A:2017 , HOH A:2020 , HOH A:2021 , HOH A:2030 , CL B:10 , CL B:20 , LAC B:23 , HOH B:2001 , HOH B:2006 , HOH B:2007 , HOH B:2008 , HOH B:2009 , HOH B:2011 , HOH B:2012 , HOH B:2013 , HOH B:2015BINDING SITE FOR CHAIN B OF VANCOMYCIN
3AC3SOFTWAREASN A:3 , GHP A:5 , OMY A:6 , 3FG A:7 , OMZ B:2BINDING SITE FOR RESIDUE CL A 21
4AC4SOFTWAREOMZ A:2 , RER A:9 , MLU B:1 , RER B:9BINDING SITE FOR RESIDUE CL B 20
5AC5SOFTWAREOMY B:6 , 3FG B:7 , HOH B:2006BINDING SITE FOR RESIDUE CL B 10
6AC6SOFTWAREHOH A:2031 , MLU B:1 , OMZ B:2 , ASN B:3 , GHP B:4 , BGC B:8 , HOH B:2006 , HOH B:2014 , HOH B:2017BINDING SITE FOR RESIDUE LAC B 23

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C0Q)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ghp A:5 -Omy A:6
2Ghp B:5 -Omy B:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C0Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1C0Q)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:7
                                     
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                   1c0q A 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG


Chain B from PDB  Type:PROTEIN  Length:7
                                     
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                   1c0q B 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1C0Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1C0Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C0Q)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1C0Q)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1aa5 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH ACETATE
1c0r CRYSTAL STRUCTURE OF VANCOMYCIN WITH D-LACTIC ACID
1fvm CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH DI-ACETYL- LYS-D-ALA-D-ALA
1gac SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT
1ghg CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON
1pn3 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXD WITH TDP AND DESVANCOSAMINYL VANCOMYCIN
1pnv CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXED WITH TDP AND VANCOMYCIN
1qd8 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL GLYCIN
1rrv CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEXED WITH TDP AND DESVANCOSAMINYL VANCOMYCIN.
1sho CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH ACETATE