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 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial AH271Homo sapiensMutation(s): 0 
Gene Names: SIRT3SIR2L3
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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ARG-HIS-LYS CD3Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
A, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
BBI
Query on BBI

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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

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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

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H
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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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 = 114.56α = 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 

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