SMTL ID : 4qa4.2 (1 other biounit)

Crystal structure of H334R HDAC8 in complex with M344

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x B3N: 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide(Non-covalent)

B3N.1: 18 residues within 4Å: Chain A: Y.100, D.101, H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, G.304, Y.306 Chain B: F.152, P.273, M.274, Y.306 Ligands: ZN.2, B3N.8 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.100, A:F.152, A:F.152, A:F.152, A:F.152, A:F.208, B:P.273 Hydrogen bonds: A:D.101, A:H.143 B3N.8: 18 residues within 4Å: Chain A: F.152, P.273, M.274, Y.306 Chain B: Y.100, D.101, H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, G.304, Y.306 Ligands: B3N.1, ZN.9 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.100, B:F.152, B:F.152, B:F.152, B:F.152, B:F.208, A:P.273 Hydrogen bonds: B:D.101, B:H.143, B:Y.306

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: B3N.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.267 ZN.9: 4 residues within 4Å: Chain B: D.178, H.180, D.267 Ligands: B3N.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.178, B:D.178, B:H.180, B:D.267

4 x K: POTASSIUM ION(Non-covalent)

K.3: 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:S.199 K.4: 4 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225 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 K.10: 6 residues within 4Å: Chain B: D.176, 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:S.199 K.11: 4 residues within 4Å: Chain B: F.189, T.192, V.195, Y.225 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.189, B:T.192, B:V.195, H2O.6, H2O.6

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Q.236, S.351, C.352, R.353 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.236, A:R.353, A:R.353 GOL.6: 6 residues within 4Å: Chain A: K.289, Y.317, V.321, G.324, K.325, T.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.324 Water bridges: A:Y.317, A:K.325, A:K.325 GOL.7: 5 residues within 4Å: Chain A: S.215, D.216, V.217, G.218, R.223 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.216, A:D.216, A:V.217, A:G.218, A:G.218, A:R.223, A:R.223 GOL.12: 4 residues within 4Å: Chain B: Q.236, S.351, C.352, R.353 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.236, B:R.353, B:R.353 GOL.13: 6 residues within 4Å: Chain B: K.289, Y.317, V.321, G.324, K.325, T.326 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.324 Water bridges: B:Y.317, B:K.325, B:K.325 GOL.14: 5 residues within 4Å: Chain B: S.215, D.216, V.217, G.218, R.223 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.216, B:V.217, B:G.218, B:G.218, B:R.223, B:R.223

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
A

Histone deacetylase 8

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