2V5W

Crystal structure of HDAC8-substrate complex

Structural Biology Knowledgebase: 2V5W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2V5W

Classification: HYDROLASE / HYDROLASE SUBSTRATE

Total Structure Weight: 88469.10

Macromolecule Entities
Molecule Chains Length Organism Details
HISTONE DEACETYLASE 8 A, B 388 Homo sapiens EC#: 3.5.1.98 IUBMB
Mutation: Y306F
Gene Name(s): HDAC8 Gene View HDACL1 CDA07
GLYCYL-GLYCYL-GLYCINE G 3 synthetic
PEPTIDIC SUBSTRATE I, L 6 synthetic

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

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

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
I, L NON-POLYMER C2 H4 O --
ALY
Query on ALY
I, L L-PEPTIDE LINKING C8 H16 N2 O3 LYS
MCM
Query on MCM
I, L NON-POLYMER C10 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.176
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 52.30 α = 90.00
b = 151.80 β = 117.02
c = 57.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-10
  • Released Date: 2007-09-04
  • Deposition author(s): Di Marco, S., Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfi, A., Defrancesco, R., Steinkuhler, C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry