Movatterモバイル変換


[0]ホーム

URL:


RCSB PDB
249,324
Structures from the PDB archive
1,068,577
Computed Structure Models (CSM)
  • PDB-101
  • wwPDB
  • EMDataResource
  • NAKB: Nucleic Acid Knowledgebase
  • wwPDB Foundation
  • PDB-IHM Logo

 4KXQ|pdb_00004kxq

Structure of NAD-dependent protein deacetylase sirtuin-1 (closed state, 1.85 A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural and Functional Analysis of Human SIRT1.

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

(2014) J Mol Biology 426: 526-541

  • PubMed24120939 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1016/j.jmb.2013.10.009
  • Primary Citation of Related Structures:  
    4IG9,4KXQ

  • PubMed Abstract: 

    SIRT1 is a NAD(+)-dependent deacetylase that plays important roles in many cellular processes. SIRT1 activity is uniquely controlled by a C-terminal regulatory segment (CTR). Here we present crystal structures of the catalytic domain of human SIRT1 in complex with the CTR in an open apo form and a closed conformation in complex with a cofactor and a pseudo-substrate peptide. The catalytic domain adopts the canonical sirtuin fold. The CTR forms a β hairpin structure that complements the β sheet of the NAD(+)-binding domain, covering an essentially invariant hydrophobic surface. The apo form adopts a distinct open conformation, in which the smaller subdomain of SIRT1 undergoes a rotation with respect to the larger NAD(+)-binding subdomain. A biochemical analysis identifies key residues in the active site, an inhibitory role for the CTR, and distinct structural features of the CTR that mediate binding and inhibition of the SIRT1 catalytic domain.


  • Organizational Affiliation
    • Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
    • Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. Electronic address: hoelz@caltech.edu.
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (APR)


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


Find Similar Assemblies

Biological assembly 1 generated by PISA (software)

PreviousNext

Macromolecule Content 

  • Total Structure Weight: 36.06 kDa 
  • Atom Count: 2,831 
  • Modeled Residue Count: 305 
  • Deposited Residue Count: 311 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-1281Homo sapiensMutation(s): 0 
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 Q96EB6 (Homo sapiens)
Explore Q96EB6 
Go to UniProtKB:  Q96EB6
PHAROS:  Q96EB6
GTEx:  ENSG00000096717 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EB6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-130Homo sapiensMutation(s): 0 
EC: 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EB6 (Homo sapiens)
Explore Q96EB6 
Go to UniProtKB:  Q96EB6
PHAROS:  Q96EB6
GTEx:  ENSG00000096717 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EB6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
E [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 (Depositor), 0.190 (DCC) 
  • R-Value Work: 0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.714α = 90
b = 92.714β = 90
c = 97.745γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references, Structure summary
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • RCSB PDB is hosted by

  • The Rutgers Artificial Intelligence and Data Science Collaboratory logo
    Uiversity of California San Diego logoSan Diego Supercomputer Center logo
    University of California San Francisco Logo

RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.


[8]ページ先頭

©2009-2026 Movatter.jp