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Structure paper

TitleHistone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Journal, issue, pagesNat. Chem. Biol., Vol. 12, Page 741-747, Year 2016
Publish dateOct 22, 2015 (structure data deposition date)
AuthorsHai, Y. / Christianson, D.W.
External linksNat. Chem. Biol. / PubMed:27454933
MethodsX-ray diffraction
Resolution1.32 - 2.79 Å
Structure data

PDB-5edu:
Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A
Method: X-RAY DIFFRACTION / Resolution: 2.79 Å

PDB-5eef:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 in complex with trichostatin A
Method: X-RAY DIFFRACTION / Resolution: 2.151 Å

PDB-5eei:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with SAHA
Method: X-RAY DIFFRACTION / Resolution: 1.32 Å

PDB-5eek:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with trichostatin A
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-5eem:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-5een:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat
Method: X-RAY DIFFRACTION / Resolution: 1.861 Å

PDB-5ef7:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with HPOB
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-5ef8:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with panobinostat
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5efb:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with oxamflatin
Method: X-RAY DIFFRACTION / Resolution: 2.543 Å

PDB-5efg:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with acetate
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-5efh:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with trifluoroketone transition state analogue
Method: X-RAY DIFFRACTION / Resolution: 2.162 Å

PDB-5efj:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with HC toxin
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-5efk:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (Y745F mutant) in complex with alpha tubulin K40 tripeptide substrate
Method: X-RAY DIFFRACTION / Resolution: 1.82 Å

PDB-5efn:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (H574A) in complex with histone H4 Lys6 tripeptide substrate
Method: X-RAY DIFFRACTION / Resolution: 1.804 Å

Chemicals

ChemComp-TSN:
TRICHOSTATIN A / antifungal, antibiotic*YM

ChemComp-ZN:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-NH4:
AMMONIUM ION

ChemComp-SO4:
SULFATE ION

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-SHH:
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE

ChemComp-GOL:
GLYCEROL

ChemComp-CL:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-IOD:
IODIDE ION

ChemComp-NA:
Unknown entry

ChemComp-FMT:
FORMIC ACID

ChemComp-5OG:
Belinostat / inhibitor*YM

ChemComp-5OJ:
4-[2-[2-hydroxyethyl(phenyl)amino]-2-oxidanylidene-ethyl]-~{N}-oxidanyl-benzamide

ChemComp-LBH:
Panobinostat / medication, inhibitor*YM

ChemComp-5OK:
Oxamflatin

ChemComp-ACT:
ACETATE ION

ChemComp-FKS:
7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol

ChemComp-BR:
BROMIDE ION

ChemComp-NO3:
NITRATE ION

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-MCM:
7-AMINO-4-METHYL-CHROMEN-2-ONE

Source
  • escherichia coli (E. coli)
  • homo sapiens (human)
  • danio rerio (zebrafish)
  • bipolaris zeicola (fungus)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / HYDROLASE

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