3C5K

Crystal structure of human HDAC6 zinc finger domain

• PDB DOI: https://doi.org/10.2210/pdb3C5K/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-31 Released: 2008-02-19 
• Deposition Author(s): Dong, A., Ravichandran, M., Schuetz, A., 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.227 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

Literature

Crystal Structure of Human HDAC6 zinc finger domain.

Dong, A., Ravichandran, M., Schuetz, A., 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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.36 kDa 
• Atom Count: 999 
• Modelled Residue Count: 108 
• Deposited Residue Count: 109 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 6	A	109	Homo sapiens	Mutation(s): 0  Gene Names: HDAC6 EC: 3.5.1 (UniProt), 3.5.1.98 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBN7 (Homo sapiens) Explore Q9UBN7  Go to UniProtKB:  Q9UBN7
PHAROS:  Q9UBN7 GTEx:  ENSG00000094631

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.227 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.5	α = 90
b = 45.109	β = 90
c = 55.759	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-19 
Deposition Author(s): Dong, A., Ravichandran, M., Schuetz, A., 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: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations