4BVG

CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527

Structural Biology Knowledgebase: 4BVG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.182

Literature

Macromolecules
Sequence Display for 4BVG

Classification: HYDROLASE / LIGASE

Total Structure Weight: 34367.68

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL A 284 Homo sapiens EC#: 3.5.1 IUBMB
Fragment: RESIDUES 116-399
Gene Name(s): SIRT3 Gene View SIR2L3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL B 10 Homo sapiens EC#: 6.2.1.1 IUBMB
Fragment: RESIDUES 638-647
Gene Name(s): ACSS1 Gene View ACAS2L KIAA1846
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
OAD
Query on OAD

B 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE
C17 H25 N5 O15 P2
BFNOPXRXIQJDHO-DLFWLGJNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.182
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 78.02 α = 90.00
b = 131.33 β = 90.00
c = 76.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-25
  • Released Date: 2013-07-17
  • Deposition author(s): Nguyen, G.T.T., Gertz, M., Weyand, M., Steegborn, C.

Revision History

  • 2013-08-07
    Type: Citation | Details: JRNL