4HD8

Crystal structure of human Sirt3 in complex with Fluor-de-Lys peptide and piceatannol

Structural Biology Knowledgebase: 4HD8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HD8

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 32624.09

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent protein deacetylase sirtuin-3, mitochondrial A 284 Homo sapiens EC#: 3.5.1 IUBMB
Fragment: UNP residues 116-399
Gene Name(s): SIRT3 Gene View SIR2L3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fluor-de-Lys peptide F 4 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PIT
Query on PIT

A PICEATANNOL
2-DIOL, (Synonym)
C14 H12 O4
CDRPUGZCRXZLFL-OWOJBTEDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPA
Query on IPA

A ISOPROPYL ALCOHOL
2-PROPANOL (Synonym)
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FDL
Query on FDL
F L-PEPTIDE LINKING C18 H23 N3 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.174
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 114.60 α = 90.00
b = 114.60 β = 90.00
c = 123.70 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-02
  • Released Date: 2012-12-05
  • Deposition author(s): Nguyen, G.T.T., Gertz, M., Steegborn, C.

Revision History

  • 2013-02-20
    Type: Citation | Details: Citation update