4HDA

Crystal structure of human Sirt5 in complex with Fluor-de-Lys peptide and resveratrol

Structural Biology Knowledgebase: 4HDA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HDA

Classification: HYDROLASE / HYDROLASE ACTIVATOR

Total Structure Weight: 60955.51

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent protein deacylase sirtuin-5, mitochondrial A, B 275 Homo sapiens EC#: 3.5.1 IUBMB
Fragment: UNP residues 34-302
Gene Name(s): SIRT5 Gene View SIR2L5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fluor-de-Lys peptide F 4 synthetic

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

B RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-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: 2.6 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.199
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 41.30 α = 90.00
b = 112.69 β = 90.05
c = 55.89 γ = 90.00

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): Gertz, M., Steegborn, C.

Revision History

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