4IF6

Structure of NAD-dependent protein deacetylase sirtuin-1 (closed state, 2.25 A)

• PDB DOI: https://doi.org/10.2210/pdb4IF6/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-14 Released: 2013-10-23 
• Deposition Author(s): Davenport, A.M., Huber, F.M., Hoelz, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.187 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 

Literature

Structure of a nucleoporin complex

Davenport, A.M., Huber, F.M., Hoelz, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 36 kDa 
• Atom Count: 2,842 
• Modelled Residue Count: 304 
• Deposited Residue Count: 312 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-1	A	281	Homo sapiens	Mutation(s): 0  Gene Names: SIR2L1, SIRT1 EC: 3.5.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EB6 (Homo sapiens) Explore Q96EB6  Go to UniProtKB:  Q96EB6
PHAROS:  Q96EB6 GTEx:  ENSG00000096717

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-1	B	31	Homo sapiens	Mutation(s): 0  Gene Names: SIRT1, SIR2L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EB6 (Homo sapiens) Explore Q96EB6  Go to UniProtKB:  Q96EB6
PHAROS:  Q96EB6 GTEx:  ENSG00000096717

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR	D [auth A]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.187 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.662	α = 90
b = 92.662	β = 90
c = 97.7	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHARP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Davenport, A.M., Huber, F.M., Hoelz, A.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2013-11-06
  Changes: Database references, Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations