SMTL ID : 4rn1.1 (1 other biounit)

Crystal structure of S39D HDAC8 in complex with a largazole analogue.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 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.267 Ligands: L8G.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.178, A:H.180, A:D.267

2 x K: POTASSIUM ION(Non-covalent)

K.2: 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.176, A:D.178, A:H.180, A:L.200 K.3: 5 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225, S.226 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.189, A:T.192, A:V.195, H2O.1, H2O.1

1 x L8G: (5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3-thia-7,10,14,20,21-pentaazatricyclo[14.3.1.1~2,5~]henicosa-1(20),2(21),16,18-tetraene-6,9,13-trione(Non-covalent)

L8G.4: 12 residues within 4Å: Chain A: Y.100, H.143, F.152, D.178, H.180, F.208, D.267, M.274, G.304, Y.306 Ligands: ZN.1, IMD.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.100, A:F.152, A:F.208, A:F.208

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 3 residues within 4Å: Chain A: P.273, M.274 Ligands: L8G.4 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: K.289, Y.317, G.320, V.321, K.325, T.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.317, A:K.325 Water bridges: A:L.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Decroos, C. et al., Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8. Biochemistry (2015)

Release Date

2015-04-08

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8

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