Macromolecule Content

Total Structure Weight: 64.98 kDa
Atom Count: 4526
Residue Count: 548
Unique protein chains: 2

5H4D

Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride

DOI: 10.2210/pdb5H4D/pdb

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

Deposited: 2016-10-31 Released: 2017-11-08
Deposition Author(s): Zhang, S., Fu, L., Liu, J., Liu, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free: 0.372
R-Value Work: 0.213
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride

Zhang, S., Fu, L., Liu, J., Liu, B.

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, H	271	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
ARG-HIS-LYS	C, D	3	Homo sapiens	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain H [A] SDF format, chain O [H] MOL2 format, chain H [A] MOL2 format, chain O [H]	A, H	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Ligand Interaction
BBI Query on BBI Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain N [H] MOL2 format, chain G [A] MOL2 format, chain N [H]	A, H	(2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone C₂₅ H₂₉ I₂ N O₃ IYIKLHRQXLHMJQ-UHFFFAOYSA-N		Ligand Interaction
FDL Query on FDL Download Ideal Coordinates CCD File SDF format, chain I [D] SDF format, chain P [C] MOL2 format, chain I [D] MOL2 format, chain P [C]	C, D	N~6~-acetyl-N-(4-methyl-2-oxo-2H-chromen-7-yl)-L-lysinamide C₁₈ H₂₃ N₃ O₄ CDFJPCDMYIJWOC-HNNXBMFYSA-N		Ligand Interaction
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [H] SDF format, chain L [H] MOL2 format, chain J [H] MOL2 format, chain L [H]	H	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain K [H] MOL2 format, chain E [A] MOL2 format, chain K [H]	A, H	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain M [H] MOL2 format, chain F [A] MOL2 format, chain M [H]	A, H	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free: 0.372
R-Value Work: 0.213
R-Value Observed: 0.220
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.56	α = 90
b = 114.56	β = 90
c = 123.404	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2016-10-31
Released Date: 2017-11-08

Deposition Author(s):

Revision History

Version 1.0: 2017-11-08
Type: Initial release
Version 1.1: 2017-11-22
Changes: Data collection

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.