1SZD

Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases

Structural Biology Knowledgebase: 1SZD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SZD

Classification: GENE REGULATION

Total Structure Weight: 35610.60

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent deacetylase HST2 A 297 Saccharomyces cerevisiae EC#: 3.5.1 IUBMB
Fragment: catalytic core domain
Gene Name(s): HST2 YPL015C LPA2C
Histone H4 peptide B 10 Saccharomyces cerevisiae Mutation: K16X
Gene Name(s): HHF1 YBR009C YBR0122 HHF2 YNL030W N2752

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)
ZN
Query on ZN

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

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
APR N/A in BindingDB
Kd: 29160 nM  BindingMOAD
Kd: 29160 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ALY
Query on ALY
B L-PEPTIDE LINKING C8 H16 N2 O3 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.214
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 105.38 α = 90.00
b = 105.38 β = 90.00
c = 66.15 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-04-05
  • Released Date: 2004-06-15
  • Deposition author(s): Zhao, K., Harshaw, R., Chai, X., Marmorstein, R.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4