5Z93

Crystal Structure of SIRT3 in complex with H3K9bhb peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report



Literature

Crystal Structure of SIRT3 in complex with H3K9bhb peptide

Zhang, X.Li, H.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial A283Homo sapiensMutation(s): 0 
Gene Names: SIRT3SIR2L3
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
NIH Common Fund Data Resources
PHAROS:  Q9NTG7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Gene for histone H3 (germline gene) B10Homo sapiensMutation(s): 0 
Find proteins for V9H1G0 (Homo sapiens)
Explore V9H1G0 
Go to UniProtKB:  V9H1G0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KHB
Query on KHB
BL-PEPTIDE LINKINGC10 H20 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.361α = 90
b = 86.025β = 90
c = 88.431γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-02 
  • Released Date: 2019-02-06 
  • Deposition Author(s): Zhang, X., Li, H.

Funding OrganizationLocationGrant Number
China--

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release