5H4D | pdb_00005h4d

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

• PDB DOI: https://doi.org/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 
  0.372 (Depositor), 0.375 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

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

Zhang, S., Fu, L., Liu, J., Liu, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.98 kDa 
• Atom Count: 4,526 
• Modeled Residue Count: 550 
• Deposited Residue Count: 550 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A, C [auth H]	271	Homo sapiens	Mutation(s): 0  Gene Names: SIRT3, SIR2L3 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7  Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7 GTEx:  ENSG00000142082

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-HIS-LYS	B [auth D], D [auth C]	4	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	H [auth A], O [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
BBI	G [auth A], N [auth H]	(2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone C25 H29 I2 N O3 IYIKLHRQXLHMJQ-UHFFFAOYSA-N
MCM	I [auth D], P [auth C]	7-AMINO-4-METHYL-CHROMEN-2-ONE C10 H9 N O2 GLNDAGDHSLMOKX-UHFFFAOYSA-N
PEG	J [auth H], L [auth H]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	E [auth A], K [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth A], M [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B [auth D], D [auth C]	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
BBI	BindingDB:  5H4D	EC50: 3250 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free:  0.372 (Depositor), 0.375 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 2017-11-08 
Deposition Author(s): Zhang, S., Fu, L., Liu, J., Liu, B.

Revision History  

• Version 1.0: 2017-11-08
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Data collection
• Version 2.0: 2023-04-05
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary