SMTL ID : 5eem.1 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: FMT.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:V.195, A:Y.228, H2O.2, H2O.4 K.3: 6 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.178, A:H.180, A:S.199, A:L.200

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: Y.228, F.359, W.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.228

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 7 residues within 4Å: Chain A: H.139, H.140, D.178, H.180, D.271, Y.311 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.140, A:Y.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hai, Y. et al., Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nat.Chem.Biol. (2016)

Release Date

2016-07-27

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Hdac6 protein

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