5H4D

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free:
0.372 (Depositor), 0.380 (DCC)
R-Value Work:
0.213 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NTG7
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

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 [auth A] SDF format, chain O [auth H] MOL2 format, chain H [auth A] MOL2 format, chain O [auth H] mmCIF format, chain H [auth A] mmCIF format, chain O [auth H]	H [auth A], O [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain O [auth H] Interactions & Density Focus chain H [auth A] Focus chain O [auth H]
BBI Query on BBI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth H] MOL2 format, chain G [auth A] MOL2 format, chain N [auth H] mmCIF format, chain G [auth A] mmCIF format, chain N [auth H]	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		Interactions Focus chain G [auth A] Focus chain N [auth H] Interactions & Density Focus chain G [auth A] Focus chain N [auth H]
MCM Query on MCM Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain P [auth C] MOL2 format, chain I [auth D] MOL2 format, chain P [auth C] mmCIF format, chain I [auth D] mmCIF format, chain P [auth C]	I [auth D], P [auth C]	7-AMINO-4-METHYL-CHROMEN-2-ONE C₁₀ H₉ N O₂ GLNDAGDHSLMOKX-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain P [auth C] Interactions & Density Focus chain I [auth D] Focus chain P [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain L [auth H] MOL2 format, chain J [auth H] MOL2 format, chain L [auth H] mmCIF format, chain J [auth H] mmCIF format, chain L [auth H]	J [auth H], L [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth H] Focus chain L [auth H] Interactions & Density Focus chain J [auth H] Focus chain L [auth H]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth H] MOL2 format, chain E [auth A] MOL2 format, chain K [auth H] mmCIF format, chain E [auth A] mmCIF format, chain K [auth H]	E [auth A], K [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth H] Interactions & Density Focus chain E [auth A] Focus chain K [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth H] MOL2 format, chain F [auth A] MOL2 format, chain M [auth H] mmCIF format, chain F [auth A] mmCIF format, chain M [auth H]	F [auth A], M [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth H] Interactions & Density Focus chain F [auth A] Focus chain M [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on 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), 0.380 (DCC)
R-Value Work: 0.213 (Depositor), 0.220 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-11-08

Deposition Author(s):

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