SMTL ID : 4qa2.3 (2 other biounits)

Crystal structure of I243N HDAC8 in complex with SAHA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 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.2: 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.3567, H2O.3567 K.5: 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.6: 5 residues within 4Å: Chain B: F.189, T.192, V.195, Y.225, S.226 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.192, B:V.195, B:Y.225, H2O.3589, H2O.3589

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.7: 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

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

SHH.4: 17 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.3, SHH.8 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.152, A:F.152, A:F.208, A:F.208, A:F.208, B:P.273, B:Y.306, B:Y.306 Hydrogen bonds: A:Y.306 SHH.8: 16 residues within 4Å: Chain A: P.273, 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.7 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.273, A:Y.306, B:F.152, B:F.152, B:F.152, B:F.208

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain B: A.270, G.271, N.310, I.348, T.349, S.351 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.270, B:N.310, B:N.310, B:T.349 GOL.10: 5 residues within 4Å: Chain B: T.69, F.70, L.163, A.188, F.189 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   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)

Peptides

Histone deacetylase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone deacetylase 8

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