2QQG

Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 2QQG

Classification: HYDROLASE

Total Structure Weight: 36835.31

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent deacetylase HST2 A 308 Saccharomyces cerevisiae EC#: 3.5.1 IUBMB
Gene Name(s): HST2 YPL015C LPA2C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B 11 Saccharomyces cerevisiae Fragment: sequence database residues 13-23
Gene Name(s): HHF1 YBR009C YBR0122 HHF2 YNL030W N2752
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A1R
Query on A1R

A 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN- 2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
C15 H24 N6 O12 P2
NDQDTBCXPOIQGT-UHNJQBFTSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NCA
Query on NCA

A NICOTINAMIDE
C6 H6 N2 O
DFPAKSUCGFBDDF-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NCA IC50: 91000 nM (100) BindingDB

N/A in BindingMoad
N/A in 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: 2.05 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.218
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 105.94 α = 90.00
b = 105.94 β = 90.00
c = 67.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-26
  • Released Date: 2007-10-09
  • Deposition author(s): Marmorstein, R., Sanders, B., Zhao, K., Slama, J.

Revision History

  • Version 1_0: 2007-10-09

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2017-10-25

    Type: Refinement description