SMTL ID : 4twj.1

The structure of Sir2Af2 bound to a myristoylated histone peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.126, C.129, C.150, C.153 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.126, A:C.129, A:C.150, A:C.153

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: N.59, P.60, R.61, Y.156 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.156 Hydrogen bonds: A:R.61 ACT.3: 4 residues within 4Å: Chain A: A.24, N.101, I.102, D.103 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.24 Hydrogen bonds: A:I.102, A:D.103 Water bridges: A:Q.100, A:N.101 ACT.4: 3 residues within 4Å: Chain A: A.24, S.192, S.193 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.24 Hydrogen bonds: A:A.24, A:S.193 Water bridges: A:L.194, A:L.194 ACT.5: 6 residues within 4Å: Chain A: G.25, F.75, N.79, K.234, A.235, G.236 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.75 Hydrogen bonds: A:N.79, A:G.236 ACT.6: 5 residues within 4Å: Chain A: K.95, A.96, R.113, E.176, E.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.176, A:E.180

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: Y.133, E.137, F.138, D.141, R.149, R.151 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.151 Water bridges: A:E.137, A:D.141, A:D.141, A:D.141, A:D.141, A:C.150 GOL.8: 3 residues within 4Å: Chain A: Y.197 Chain B: R.10, R.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.10, B:R.12 Water bridges: B:R.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ringel, A.E. et al., Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2. Protein Sci. (2014)

Release Date

2014-12-03

Peptides

NAD-dependent protein deacylase 2: A
Histone H4 peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacylase 2

Histone H4 peptide

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