SMTL ID : 2od2.2 (1 other biounit)

Crystal Structure of yHst2 I117F mutant bound to carba-NAD+ and an acetylated H4 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.157, C.160, C.184, C.187 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.157, A:C.160, A:C.184, A:C.187 ZN.7: 4 residues within 4Å: Chain C: C.157, C.160, C.184, C.187 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.157, C:C.160, C:C.184, C:C.187

2 x CNA: CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

CNA.2: 25 residues within 4Å: Chain A: G.46, A.47, G.48, S.50, T.51, I.55, F.58, R.59, Q.129, N.130, F.131, D.132, F.198, G.237, T.238, S.239, V.242, N.262, L.263, E.264, Q.282, Y.283, S.284 Chain B: K.5 Chain C: P.61 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.47 Hydrogen bonds: A:A.47, A:T.51, A:Q.129, A:F.131, A:D.132, A:D.132, A:D.132, A:G.237, A:S.239, A:S.239, A:N.262, A:L.263, A:E.264, A:S.284 Water bridges: A:T.51, A:R.59, A:R.59, A:L.240, A:E.264, A:E.264 Salt bridges: A:R.59 CNA.8: 25 residues within 4Å: Chain A: P.61 Chain C: G.46, A.47, G.48, S.50, T.51, I.55, F.58, R.59, Q.129, N.130, F.131, D.132, F.198, G.237, T.238, S.239, V.242, N.262, L.263, E.264, Q.282, Y.283, S.284 Chain D: K.5 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:A.47 Hydrogen bonds: C:A.47, C:T.51, C:T.51, C:Q.129, C:F.131, C:D.132, C:D.132, C:G.237, C:T.238, C:S.239, C:S.239, C:N.262, C:L.263, C:E.264, C:S.284 Water bridges: C:T.51, C:D.57, C:R.59, C:R.59, C:E.78, C:E.78, C:L.240, C:E.264 Salt bridges: C:R.59

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.206, S.207, W.210, S.247, E.251 Chain B: K.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.207, A:W.210, A:S.247, A:S.247 GOL.4: 4 residues within 4Å: Chain A: P.56, T.63, G.64, E.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.63, A:T.63, A:E.99 GOL.5: 6 residues within 4Å: Chain A: K.98, Y.101, N.104, K.170, L.173, A.174 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.98, A:N.104, A:L.173 Water bridges: A:K.170, A:K.170, A:A.174 GOL.6: 4 residues within 4Å: Chain A: K.40, K.124, W.216, K.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.40, A:K.124, A:K.124, A:K.220, A:K.220 GOL.9: 6 residues within 4Å: Chain C: F.206, S.207, W.210, S.247, E.251 Chain D: K.1 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.207, C:W.210, C:S.247, C:S.247 Water bridges: C:E.251 GOL.10: 4 residues within 4Å: Chain C: P.56, T.63, G.64, E.99 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.63, C:E.99 GOL.11: 6 residues within 4Å: Chain C: K.98, Y.101, N.104, K.170, L.173, A.174 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.98, C:N.104, C:L.173 Water bridges: C:K.170, C:K.170, C:A.174 GOL.12: 4 residues within 4Å: Chain C: K.40, K.124, W.216, K.220 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.40, C:K.124, C:K.124, C:K.220, C:K.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanders, B.D. et al., Structural basis for nicotinamide inhibition and base exchange in sir2 enzymes. Mol.Cell (2007)

Release Date

2007-02-20

Peptides

NAD-dependent deacetylase HST2: AC
Acetylated H4 peptide: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

NAD-dependent deacetylase HST2

Acetylated H4 peptide

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