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

Crystal structure of I243N HDAC8 in complex with SAHA

Coordinates

PDB Format Compare

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.1, H2O.1 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.5, H2O.5

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 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:P.273, B:Y.306, B:Y.306, A:F.152, A:F.152, A:F.208, A:F.208, A:F.208 Hydrogen bonds: A:H.143, 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 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.273, A:Y.306, B:F.152, B:F.152, B:F.152, B:F.208 Hydrogen bonds: B:H.143

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   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

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