6ACL

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2AK95

PDB DOI: https://doi.org/10.2210/pdb6ACL/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

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

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.

Macromolecule Content

Total Structure Weight: 30.36 kDa
Atom Count: 2,286
Modelled Residue Count: 277
Deposited Residue Count: 277
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	267	Homo sapiens	Mutation(s): 0 Gene Names: SIRT5, SIR2L5 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXA8 (Homo sapiens) Explore Q9NXA8 Go to UniProtKB: Q9NXA8
PHAROS: Q9NXA8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NXA8
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
succinyl peptide H2AK95	B	10	Homo sapiens	Mutation(s): 0 Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908
PHAROS: P04908
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04908
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SLL Query on SLL	B	L-PEPTIDE LINKING	C₁₀ H₁₈ N₂ O₅		LYS

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 = 55.937	α = 90
b = 42.807	β = 109.25
c = 61.591	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	2017YFA0503600
	China	2016YFA0400903
	China	XDB19000000
	China	31621002
	China	U1532109
	China	31700671
	China	2017FXCX004
	China	1608085QC52

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.