3GV4

Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.174

Literature

Macromolecules
Sequence Display for 3GV4

Classification: HYDROLASE

Total Structure Weight: 12819.71

Macromolecule Entities
Molecule Chains Length Organism Details
Histone deacetylase 6 A 107 Homo sapiens EC#: 3.5.1.98 IUBMB
Fragment: UNP residues 1109-1215
Gene Name(s): HDAC6 Gene View KIAA0901 JM21
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ubiquitin C-terminal peptide RLRGG H 5 synthetic

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

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.174
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 31.66 α = 90.00
b = 36.09 β = 90.00
c = 89.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-30
  • Released Date: 2009-04-28
  • Deposition author(s): Dong, A., Ravichandran, M., Loppnau, P., Li, Y., MacKenzie, F., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Dhe-Paganon, S., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

Revision History

  • Version 1_0: 2009-04-28

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2017-11-01

    Type: Refinement description