SMTL ID : 5d7o.1

Crystal structure of Sirt2-ADPR at an improved resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.149, C.154, C.175, C.178 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.149, A:C.154, A:C.175, A:C.178 ZN.3: 4 residues within 4Å: Chain B: C.149, C.154, C.175, C.178 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.149, B:C.154, B:C.175, B:C.178

2 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.2: 21 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, F.189, G.215, T.216, S.217, V.220, N.240, K.241, E.242, G.276, E.277, C.278 20 PLIP interactions: 20 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:Q.121, A:T.216, A:S.217, A:S.217, A:N.240, A:K.241, A:E.242, A:C.278 Water bridges: A:S.44, A:D.279 Salt bridges: A:R.51, A:R.51 AR6.4: 21 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, F.189, G.215, T.216, S.217, V.220, N.240, K.241, E.242, G.276, E.277, C.278 22 PLIP interactions: 22 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:Y.58, B:Y.58, B:Q.121, B:H.141, B:S.217, B:S.217, B:N.240, B:K.241, B:E.242, B:E.242, B:C.278 Water bridges: B:S.44, B:E.277, B:D.279 Salt bridges: B:R.51, B:R.51

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 5 residues within 4Å: Chain B: K.243, D.264, A.273, W.274, L.275 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.243, B:K.243, B:L.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rumpf, T. et al., Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking. Acta Crystallogr.,Sect.F (2015)

Release Date

2015-12-02

Peptides

NAD-dependent protein deacetylase sirtuin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-2