SMTL ID : 9gz5.1

X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-5-dodecenoic acid.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.164, H.166, D.240 Ligands: 01.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.164, A:D.164, A:H.166, A:D.240

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: M.129, R.132, F.173, K.194, E.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.132, A:K.194, A:E.196 Water bridges: A:R.132 GOL.3: 2 residues within 4Å: Chain A: D.287, D.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.287, A:D.287, A:D.290

1 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: D.162, D.164, H.166, S.185, M.186, H.187 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.162, A:D.162, A:D.164, A:H.166, A:S.185

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: T.83, Q.84, S.86, E.87, L.88, P.89, L.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.86, A:E.87, A:L.88, A:L.90 EDO.6: 3 residues within 4Å: Chain A: S.63, L.64, H.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.66

1 x 01: cis-5-dodecenoic acid

01.7: 20 residues within 4Å: Chain A: Y.19, L.21, F.28, A.30, Y.33, S.97, F.98, G.124, F.125, H.126, H.127, F.136, C.137, D.164, H.166, D.240, A.281, G.282, Y.284 Ligands: ZN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.21, A:F.28, A:F.28, A:F.28, A:F.28, A:A.30, A:Y.33, A:F.98, A:F.125, A:F.136 Salt bridges: A:H.126, A:H.127, A:H.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Novakova, Z. et al., X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-5-dodecenoic acid. To Be Published

Release Date

2025-10-15

Peptides

Histone deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase