5H4D

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

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 

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This is version 2.0 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrialA,
C [auth H]		271Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ARG-HIS-LYSB [auth D],
D [auth C]		4Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
H [auth A],
O [auth H]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
BBI
Query on BBI
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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
Query on MCM
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I [auth D],
P [auth C]		7-AMINO-4-METHYL-CHROMEN-2-ONE
C10 H9 N O2
GLNDAGDHSLMOKX-UHFFFAOYSA-N
PEG
Query on PEG
Download Ideal Coordinates CCD File 
J [auth H],
L [auth H]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
K [auth H]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
F [auth A],
M [auth H]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY		B [auth D],
D [auth C]		L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Binding Affinity Annotations 
IDSourceBinding 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 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.220 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.56α = 90
b = 114.56β = 90
c = 123.404γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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