1FVM

Complex of vancomycin with DI-acetyl-LYS-D-ALA-D-ALA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structures of the Complexes between Vancomycin and Cell-Wall Precursor Analogs.

Nitanai, Y.Kikuchi, T.Kakoi, K.Hanamaki, S.Fujisawa, I.Aoki, K.

(2009) J.Mol.Biol. 385: 1422

  • DOI: 10.1016/j.jmb.2008.10.026

  • PubMed Abstract: 
  • The crystal structures of three vancomycin complexes with two vancomycin-sensitive cell-wall precursor analogs (diacetyl-Lys-D-Ala-D-Ala and acetyl-D-Ala-D-Ala) and a vancomycin-resistant cell-wall precursor analog (diacetyl-Lys-D-Ala-D-lactate) were ...

    The crystal structures of three vancomycin complexes with two vancomycin-sensitive cell-wall precursor analogs (diacetyl-Lys-D-Ala-D-Ala and acetyl-D-Ala-D-Ala) and a vancomycin-resistant cell-wall precursor analog (diacetyl-Lys-D-Ala-D-lactate) were determined at atomic resolutions of 1.80 A, 1.07 A, and 0.93 A, respectively. These structures not only reconfirm the "back-to-back" dimerization of vancomycin monomers and the ligand-binding scheme proposed by previous experiments but also show important structural features of strategies for the generation of new glycopeptide antibiotics. These structural features involve a water-mediated antibiotic-ligand interaction and supramolecular structures such as "side-by-side" arranged dimer-to-dimer structures, in addition to ligand-mediated and "face-to-face" arranged dimer-to-dimer structures. In the diacetyl-Lys-D-Ala-D-lactate complex, the interatomic O...O distance between the carbonyl oxygen of the fourth residue of the antibiotic backbone and the ester oxygen of the D-lactate moiety of the ligand is clearly longer than the corresponding N-H...O hydrogen-bonding distance observed in the two other complexes due to electrostatic repulsion. In addition, two neighboring hydrogen bonds are concomitantly lengthened. These observations provide, at least in part, a molecular basis for the reduced antibacterial activity of vancomycin toward vancomycin-resistant bacteria with cell-wall precursors terminating in -D-Ala-D-lactate.


    Organizational Affiliation

    Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan. nitanai@spring8.or.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VANCOMYCIN
A, B, C, D, E, F
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DI-ACETYL-LYS-D-ALA-D-ALA
G, H, I, J, K, L
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B, C, D, E, F
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
RER
Query on RER

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose
VANCOSAMINE
C7 H15 N O3
OIJZDPGKNVKVBL-WNJXEPBRSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
A,B,C,D,E,FVANCOMYCINGlycopeptide / Antibiotic

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Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DAL
Query on DAL
G, H, I, J, K, L
D-PEPTIDE LINKINGC3 H7 N O2

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DLS
Query on DLS
G, H, I, J, K, L
L-PEPTIDE LINKINGC10 H18 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.637α = 90.00
b = 36.425β = 90.00
c = 65.728γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
MOSFLMdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-01
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other