SMTL ID : 1q17.1

Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.149, C.152, C.176, C.179 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.149, A:C.152, A:C.176, A:C.179 ZN.4: 5 residues within 4Å: Chain B: C.149, C.152, C.176, V.178, C.179 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.149, B:C.152, B:C.176, B:C.179 ZN.8: 5 residues within 4Å: Chain C: C.149, C.152, C.176, V.178, C.179 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.149, C:C.152, C:C.176, C:C.179

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: R.210, R.246 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: K.32, W.208 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: R.210, R.246 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain C: R.210, R.246 Ligand excluded by PLIP

3 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.3: 20 residues within 4Å: Chain A: G.38, A.39, G.40, T.43, D.49, F.50, R.51, Y.58, Q.121, H.141, G.229, T.230, S.231, V.234, N.254, L.255, E.256, Q.274, Y.275, S.276 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:A.39, A:G.40, A:T.43, A:F.50, A:R.51, A:R.51, A:Y.58, A:Q.121, A:G.229, A:T.230, A:S.231, A:N.254, A:L.255, A:E.256, A:E.256, A:S.276, A:S.276 Salt bridges: A:R.51, A:R.51 APR.7: 20 residues within 4Å: Chain B: G.38, A.39, G.40, T.43, D.49, F.50, R.51, Y.58, Q.121, H.141, G.229, T.230, S.231, V.234, N.254, L.255, E.256, Q.274, Y.275, S.276 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.39, B:T.43, B:T.43, B:F.50, B:R.51, B:R.51, B:Q.121, B:Q.121, B:T.230, B:S.231, B:N.254, B:L.255, B:S.276 Water bridges: B:S.52, B:V.188, B:D.277 Salt bridges: B:R.51, B:R.51 APR.10: 20 residues within 4Å: Chain A: M.7 Chain C: G.38, A.39, G.40, T.43, D.49, F.50, R.51, Y.58, Q.121, H.141, G.229, T.230, S.231, V.234, N.254, L.255, Q.274, Y.275, S.276 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:A.39, C:F.50, C:R.51, C:R.51, C:Q.121, C:Q.121, C:T.230, C:S.231, C:N.254, C:L.255, C:S.276, C:S.276 Salt bridges: C:R.51, C:R.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, K. et al., Structure of the Yeast Hst2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl ADP Ribose and Histone Peptide. Structure (2003)

Release Date

2003-11-18

Peptides

HST2 protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HST2 protein