3GV4

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

• PDB DOI: https://doi.org/10.2210/pdb3GV4/pdb

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


• Deposited: 2009-03-30 Released: 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.230 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

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

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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.82 kDa 
• Atom Count: 1,008 
• Modelled Residue Count: 103 
• Deposited Residue Count: 112 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 6	A	107	Homo sapiens	Mutation(s): 0  Gene Names: HDAC6, KIAA0901, JM21 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBN7 (Homo sapiens) Explore Q9UBN7  Go to UniProtKB:  Q9UBN7
PHAROS:  Q9UBN7 GTEx:  ENSG00000094631

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin C-terminal peptide RLRGG	B [auth H]	5	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.230 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.657	α = 90
b = 36.093	β = 90
c = 88.998	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASES	phasing
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description