8V15 | pdb_00008v15

Human SIRT3 bound to p53-AMC peptide, Carba-NAD, and Honokiol

• PDB DOI: https://doi.org/10.2210/pdb8V15/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-11-19 Released: 2023-12-06 
• Deposition Author(s): Chakrabarti, R., Ghosh, A., Guan, X., Upadhyay, A., Dumpati, R.K., Munshi, S., Roy, S., Chall, S., Rahnamoun, A., Reverdy, C., Errasti, G., Delacroix, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.303 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Computationally Driven Discovery and Characterization of SIRT3 Activating Compounds that Fully Recover Catalytic Activity under NAD+ Depletion

Chakrabarti, R., Ghosh, A., Guan, X., Upadhyay, A., Dumpati, R.K., Munshi, S., Roy, S., Chall, S., Rahnamoun, A., Reverdy, C., Errasti, G., Delacroix, T.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.11.09.566481

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.8 kDa 
• Atom Count: 4,442 
• Modeled Residue Count: 549 
• Deposited Residue Count: 572 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A, C	282	Homo sapiens	Mutation(s): 0  Gene Names: SIRT3 EC: 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
GLN-PRO-LYS-FDL	B, D	4	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CNA	F [auth A], I [auth C]	CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE C22 H30 N7 O13 P2 DGPLSUKWXXSBCU-VGXGLJSLSA-O
Y4T (Subject of Investigation/LOI)	H [auth C]	(1P)-3',5-di(prop-2-en-1-yl)[1,1'-biphenyl]-2,4'-diol C18 H18 O2 FVYXIJYOAGAUQK-UHFFFAOYSA-N
ZN	E [auth A], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FDL	B, D	L-PEPTIDE LINKING	C18 H23 N3 O4		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
CNA	BindingDB:  8V15	Kd: min: 6600, max: 7300 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.303 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.683	α = 90
b = 159.432	β = 90.61
c = 53.047	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Chakrabarti, R., Ghosh, A., Guan, X., Upadhyay, A., Dumpati, R.K., Munshi, S., Roy, S., Chall, S., Rahnamoun, A., Reverdy, C., Errasti, G., Delacroix, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release