5XHS

Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate SuBKA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report



Literature

Interactions between sirtuins and fluorogenic small-molecule substrates offer insights into inhibitor design

Wang, H.L.Liu, S.Yu, Z.J.Wu, C.Cheng, L.Wang, Y.Chen, K.Zhou, S.Chen, Q.Yu, Y.Li, G.B.

(2017) RSC Adv 7: 36214-36222


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacylase sirtuin-5, mitochondrial
A
288Homo sapiensMutation(s): 0 
Gene Names: SIRT5SIR2L5
EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q9NXA8 (Homo sapiens)
Go to UniProtKB:  Q9NXA8
NIH Common Fund Data Resources
PHAROS  Q9NXA8
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SLL
Query on SLL

Download CCD File 
A
(2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid
C10 H18 N2 O5
ZAFOVBXOMIXMTH-ZETCQYMHSA-N
 Ligand Interaction
MCM
Query on MCM

Download CCD File 
A
7-AMINO-4-METHYL-CHROMEN-2-ONE
C10 H9 N O2
GLNDAGDHSLMOKX-UHFFFAOYSA-N
 Ligand Interaction
PHQ
Query on PHQ

Download CCD File 
A
benzyl chlorocarbonate
C8 H7 Cl O2
HSDAJNMJOMSNEV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.13α = 90
b = 55.274β = 90
c = 124.303γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-04-24 
  • Released Date: 2018-05-02 
  • Deposition Author(s): Yu, Y., Li, B., Chen, Q.

Funding OrganizationLocationGrant Number
China--

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release