Macromolecule Content

Total Structure Weight: 67.23 kDa
Atom Count: 4995
Residue Count: 560
Unique protein chains: 2

5Z94

Crystal Structure of SIRT3 in complex with H3K4bhb peptide

DOI: 10.2210/pdb5Z94/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-02-02 Released: 2019-02-06
Deposition Author(s): Zhang, X., Li, H.

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

Literature

Crystal Structure of SIRT3 in complex with H3K4bhb peptide

Zhang, X., Li, H.

To be published.

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A, B	283	Homo sapiens	Mutation(s): 0 Gene Names: SIRT3, SIR2L3 EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7 Go to UniProtKB: Q9NTG7
NIH Common Fund Data Resources
PHAROS: Q9NTG7 GTEx: ENSG00000142082
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gene for histone H3 (germline gene)	C, D	15	Homo sapiens	Mutation(s): 0
Find proteins for V9H1G0 (Homo sapiens) Explore V9H1G0 Go to UniProtKB: V9H1G0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain I [A] SDF format, chain M [B] MOL2 format, chain I [A] MOL2 format, chain M [B]	A, B	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [A] SDF format, chain L [B] MOL2 format, chain H [A] MOL2 format, chain L [B]	A, B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain K [B] SDF format, chain N [D] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain K [B] MOL2 format, chain N [D]	A, B, D	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain J [B] MOL2 format, chain E [A] MOL2 format, chain J [B]	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KHB Query on KHB	C,D	L-PEPTIDE LINKING	C₁₀ H₂₀ N₂ O₄		LYS

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 = 75.472	α = 90
b = 76.26	β = 115.77
c = 75.425	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Deposited Date: 2018-02-02
Released Date: 2019-02-06

Deposition Author(s):

Revision History

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

RCSB PDB is 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.