4KXQ

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

Structural Biology Knowledgebase: 4KXQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.168

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KXQ

Classification: HYDROLASE

Total Structure Weight: 36058.03

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent protein deacetylase sirtuin-1 A 281 Homo sapiens EC#: 3.5.1 IUBMB
Fragment: deacetylase domain (UNP residues 234-510)
Gene Name(s): SIRT1 Gene View SIR2L1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NAD-dependent protein deacetylase sirtuin-1 B 30 Homo sapiens EC#: 3.5.1 IUBMB
Fragment: UNP residues 641-663
Gene Name(s): SIRT1 Gene View SIR2L1

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
APR
Query on APR

A ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.168
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 92.71 α = 90.00
b = 92.71 β = 90.00
c = 97.75 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-27
  • Released Date: 2013-10-23
  • Deposition author(s): Davenport, A.M., Huber, F.M., Hoelz, A.

Revision History

  • 2014-02-05
    Type: Citation | Details: Citation update
  • 2013-11-06
    Type: Citation | Details: Citation update
  • 2013-11-06
    Type: Entry title | Details: Title corrected