5ZGC

Crystal Structure of SIRT3 in complex with H4K16bhb peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 

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 H4K16bhb peptide

Li, H.Zhang, X.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A, B, C, D, E, F
274Homo sapiensMutation(s): 0 
Gene Names: SIRT3 (SIR2L3)
EC: 3.5.1.-
Find proteins for Q9NTG7 (Homo sapiens)
Go to Gene View: SIRT3
Go to UniProtKB:  Q9NTG7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4K16bhb peptide
G, H, I, J, K, L
11Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KHB
Query on KHB
G, H, I, J, K, L
L-peptide linkingC10 H20 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 138.512α = 90.00
b = 138.512β = 90.00
c = 242.876γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
Cootmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-03-08 
  • Released Date: 2019-04-03 
  • Deposition Author(s): Li, H., Zhang, X.

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release