SMTL ID : 1t64.2 (1 other biounit)

Crystal Structure of human HDAC8 complexed with Trichostatin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: TSN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.178, A:H.180, A:D.267

2 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.3: 1 residues within 4Å: Chain A: A.68 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.68, H2O.6, H2O.7, H2O.7

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 7 residues within 4Å: Chain A: D.176, L.177, D.178, H.180, S.199, L.200, H.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.176, A:L.200, A:L.200 NA.5: 4 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.192, A:Y.225

2 x TSN: TRICHOSTATIN A(Non-covalent)

TSN.6: 14 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, M.274, Y.306 Ligands: ZN.1, TSN.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.100, A:F.152, A:F.152, A:F.208 Hydrogen bonds: A:H.143, A:Y.306 TSN.7: 10 residues within 4Å: Chain A: I.34, P.35, R.37, Y.111, W.141, F.152, P.273, M.274, Y.306 Ligands: TSN.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.35, A:P.273, A:Y.306, A:Y.306, A:Y.306 pi-Stacking: A:F.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Somoza, J.R. et al., Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases. Structure (2004)

Release Date

2004-07-27

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 8

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