5Z94

Crystal Structure of SIRT3 in complex with H3K4bhb peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal Structure of SIRT3 in complex with H3K4bhb peptide

Zhang, X.Li, H.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A, B
283Homo sapiensMutation(s): 0 
Gene Names: SIRT3SIR2L3
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7
GTEx:  ENSG00000142082 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gene for histone H3 (germline gene)
C, D
15Homo sapiensMutation(s): 0 
UniProt
Find proteins for V9H1G0 (Homo sapiens)
Explore V9H1G0 
Go to UniProtKB:  V9H1G0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9H1G0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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F [auth A],
G [auth A],
K [auth B],
N [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KHB
Query on KHB
C, D
L-PEPTIDE LINKINGC10 H20 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.472α = 90
b = 76.26β = 115.77
c = 75.425γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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