5WGK

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with HPB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Unusual Zinc Binding Mode of HDAC6-Selective Hydroxamate Inhibitors

Porter, N.J.Mahendran, A.Breslow, R.Christianson, D.W.

(2017) Proc.Natl.Acad.Sci.Usa --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hdac6 protein
A
364Danio rerioGene Names: hdac6
Find proteins for A7YT55 (Danio rerio)
Go to UniProtKB:  A7YT55
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
AGJ
Query on AGJ

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A
N-hydroxy-4-{[(2-hydroxyethyl)(phenylacetyl)amino]methyl}benzamide
C18 H20 N2 O4
GTFAUKGKYICUDS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.149 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.670α = 90.00
b = 83.970β = 90.00
c = 94.570γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM49758

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release