2HJH | pdb_00002hjh

Crystal Structure of the Sir2 deacetylase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.215 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.187 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted XYQClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


Literature

Autoregulation of the yeast Sir2 deacetylase by reaction and trapping of a pseudosubstrate motif in the active site

Hall, B.E., Buchberger, J.R., Gerber, S.A., Ambrosio, A.L.B., Gygi, S.P., Filman, D., Moazed, D., Ellenberger, T.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent histone deacetylase SIR2
A, B
354Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SIR2, MAR1
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt
Find proteins for P06700 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06700 
Go to UniProtKB:  P06700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06700
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYQ
Query on XYQ
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE
C17 H25 N5 O15 P2
IJOUKWCBVUMMCR-DLFWLGJNSA-N
NCA
Query on NCA
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		NICOTINAMIDE
C6 H6 N2 O
DFPAKSUCGFBDDF-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
NCA BindingDB:  2HJH IC50: 5.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.215 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.187 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.353α = 90
b = 89.566β = 104.95
c = 94.51γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted XYQClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary