6ACL

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2AK95


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report



Literature

complex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H2AK95

Hang, T.R.Chen, W.B.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacylase sirtuin-5, mitochondrial
A
267Homo 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
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
succinyl peptide H2AK95
B
10Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SLL
Query on SLL
BL-PEPTIDE LINKINGC10 H18 N2 O5LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.937α = 90
b = 42.807β = 109.25
c = 61.591γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-26 
  • Released Date: 2019-07-24 
  • Deposition Author(s): Hang, T.R., Chen, W.B.

Funding OrganizationLocationGrant Number
China2017YFA0503600
China2016YFA0400903
ChinaXDB19000000
China31621002
ChinaU1532109
China31700671
China2017FXCX004
China1608085QC52

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release