SMTL ID : 4qa0.1

Crystal structure of C153F HDAC8 in complex with SAHA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: SHH.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.178, A:H.180, A:D.267 ZN.5: 4 residues within 4Å: Chain B: D.178, H.180, D.267 Ligands: SHH.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.178, B:H.180, B:D.267

4 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: D.176, L.177, 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:T.192, A:V.195, A:Y.225, H2O.1, H2O.1 K.6: 7 residues within 4Å: Chain B: D.176, L.177, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.176, B:D.176, B:D.178, B:H.180, B:L.200 K.7: 5 residues within 4Å: Chain B: F.189, T.192, V.195, Y.225, S.226 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.189, B:V.195, B:Y.225, H2O.17

2 x SHH: OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE(Non-covalent)

SHH.4: 18 residues within 4Å: Chain A: Y.100, H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, M.274, G.304, Y.306 Chain B: P.273, M.274, Y.306 Ligands: ZN.1, SHH.8, GOL.9 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.152, A:F.152, A:F.208, A:F.208, B:P.273, B:P.273, B:Y.306, B:Y.306 Hydrogen bonds: A:H.142, A:H.143, A:Y.306 Water bridges: A:D.101, A:D.101 SHH.8: 18 residues within 4Å: Chain A: P.273, M.274, Y.306 Chain B: Y.100, H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, M.274, G.304, Y.306 Ligands: SHH.4, ZN.5, GOL.9 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.152, B:F.152, B:F.152, B:F.152, B:F.208, B:F.208, B:F.208, A:P.273, A:Y.306 Hydrogen bonds: B:H.143, B:Y.306 Water bridges: B:D.101, B:D.101

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: K.33, F.152 Chain B: K.33, F.152 Ligands: SHH.4, SHH.8 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.33, B:K.33, A:K.33 Water bridges: B:K.33, A:K.33 GOL.10: 5 residues within 4Å: Chain B: A.68, F.70, H.71, T.72, D.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.73 Water bridges: B:F.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Decroos, C. et al., Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders. Acs Chem.Biol. (2014)

Release Date

2014-08-06

Peptides

Histone deacetylase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone deacetylase 8