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


This is version 1.0 of the entry. See complete history


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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacylase sirtuin-5, mitochondrialA267Homo sapiensMutation(s): 0 
Gene Names: SIRT5SIR2L5
EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q9NXA8 (Homo sapiens)
Explore Q9NXA8 
Go to UniProtKB:  Q9NXA8
NIH Common Fund Data Resources
PHAROS:  Q9NXA8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
succinyl peptide H2AK95B10Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS:  P04908
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 
C [auth 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  (Full details and data files)

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