SMTL ID : 7qno.1

Crystal structure of ligand-free Danio rerio HDAC6 CD1 CD2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x PRO: PROLINE(Non-covalent)

PRO.1: 2 residues within 4Å: Chain A: S.814, L.815 1 PLIP interactions: 1 interactions with chain A, Hydrogen bonds: A:L.815

4 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.236, H.238, D.329, G.367, Y.369 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.236, A:D.236, A:H.238, A:D.329, A:Y.369 K.3: 8 residues within 4Å: Chain A: D.234, D.236, H.238, H.239, G.240, S.257, V.258, H.259 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.234, A:D.236, A:H.238, A:S.257, A:V.258 K.5: 8 residues within 4Å: Chain A: D.616, D.618, H.620, H.621, G.622, S.639, L.640, H.641 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.616, A:D.616, A:D.616, A:H.620, A:S.639 K.6: 6 residues within 4Å: Chain A: F.247, D.250, V.253, L.254, Y.286, N.287 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.247, A:D.250, A:V.253, A:Y.286

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 7 residues within 4Å: Chain A: H.579, D.618, V.619, H.620, D.711, G.749, Y.751 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.618, A:D.618, A:H.620, A:D.711, H2O.1

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: A.118, V.119, T.120, E.121, L.124, K.137, F.164, C.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.119, A:K.137 GOL.8: 10 residues within 4Å: Chain A: H.392, C.440, A.441, V.443, L.563, T.606, R.607, L.610, E.702, R.742 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.441, A:L.563, A:R.607, A:E.702, A:R.742, A:R.742 GOL.9: 8 residues within 4Å: Chain A: V.331, I.332, G.333, P.343, N.370, Q.372, S.373, E.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.332, A:S.373 GOL.10: 3 residues within 4Å: Chain A: T.104, E.105, R.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.104, A:E.105 GOL.11: 3 residues within 4Å: Chain A: G.106, G.109, R.110 No protein-ligand interaction detected (PLIP) GOL.12: 3 residues within 4Å: Chain A: D.263, G.264, S.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.263, A:D.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langousis, G. et al., Expression and Crystallization of HDAC6 Tandem Catalytic Domains. Methods Mol.Biol. (2023)

Release Date

2022-02-09

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6