1JU2

Crystal structure of the hydroxynitrile lyase from almond


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The hydroxynitrile lyase from almond: a lyase that looks like an oxidoreductase.

Dreveny, I.Gruber, K.Glieder, A.Thompson, A.Kratky, C.

(2001) Structure 9: 803-815

  • Also Cited By: 3GDN

  • PubMed Abstract: 
  • Cyanogenesis is a defense process of several thousand plant species. Hydroxynitrile lyase, a key enzyme of this process, cleaves a cyanohydrin into hydrocyanic acid and the corresponding aldehyde or ketone. The reverse reaction constitutes an importa ...

    Cyanogenesis is a defense process of several thousand plant species. Hydroxynitrile lyase, a key enzyme of this process, cleaves a cyanohydrin into hydrocyanic acid and the corresponding aldehyde or ketone. The reverse reaction constitutes an important tool in biocatalysis. Different classes of hydroxynitrile lyases have convergently evolved from FAD-dependent oxidoreductases, alpha/beta hydrolases, and alcohol dehydrogenases. The FAD-dependent hydroxynitrile lyases (FAD-HNLs) carry a flavin cofactor whose redox properties appear to be unimportant for catalysis.


    Organizational Affiliation

    Institut für Chemie, Karl-Franzens-Universität, Heinrichstrasse 28, Graz A-8010, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hydroxynitrile lyase
A, B
536Prunus dulcisGene Names: MDL2 (HNL1)
EC: 4.1.2.10
Find proteins for Q945K2 (Prunus dulcis)
Go to UniProtKB:  Q945K2
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.160 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 56.176α = 79.57
b = 67.494β = 77.78
c = 79.796γ = 67.19
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance