SMTL ID : 5d7p.1

Crystal structure of human Sirt2 in complex with ADPR and EX-243

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.143, C.148, C.169, C.172 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.143, A:C.148, A:C.169, A:C.172 ZN.5: 4 residues within 4Å: Chain B: C.143, C.148, C.169, C.172 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.143, B:C.148, B:C.169, B:C.172

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: 24 residues within 4Å: Chain A: G.32, A.33, G.34, T.37, D.43, F.44, R.45, S.46, Y.52, Q.115, H.135, F.183, G.209, T.210, S.211, V.214, N.234, K.235, E.236, G.270, E.271, C.272 Chain B: L.245 Ligands: OCZ.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.33, A:G.34, A:T.37, A:T.37, A:F.44, A:R.45, A:Y.52, A:Y.52, A:Q.115, A:Q.115, A:H.135, A:S.211, A:N.234, A:K.235, A:E.236, A:E.236, A:C.272 Water bridges: A:T.37, A:E.271, A:D.273 Salt bridges: A:R.45, A:R.45, A:R.45 AR6.6: 24 residues within 4Å: Chain B: G.32, A.33, G.34, T.37, D.43, F.44, R.45, S.46, Y.52, Q.115, H.135, F.183, G.209, T.210, S.211, V.214, N.234, K.235, E.236, G.270, E.271, C.272 Ligands: OCZ.8, PEG.9 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:A.33, B:G.34, B:T.37, B:T.37, B:F.44, B:R.45, B:R.45, B:Y.52, B:Q.115, B:Q.115, B:T.210, B:S.211, B:N.234, B:K.235, B:E.236, B:E.271, B:C.272 Water bridges: B:T.37, B:D.273 Salt bridges: B:R.45, B:R.45

4 x OCZ: (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide(Non-covalent)

OCZ.3: 12 residues within 4Å: Chain A: I.41, F.79, A.83, L.86, Y.87, P.88, G.89, F.91, I.117, D.118, F.138 Ligands: OCZ.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.41, A:I.41, A:L.86, A:Y.87, A:I.117, A:D.118 Hydrogen bonds: A:G.89 Water bridges: A:F.91 OCZ.4: 14 residues within 4Å: Chain A: I.41, P.42, F.44, F.67, Q.115, N.116, I.117, D.118, H.135, I.180, V.181, F.182 Ligands: AR6.2, OCZ.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.41, A:F.44, A:I.117, A:I.117, A:I.117, A:H.135 Hydrogen bonds: A:Q.115, A:I.117, A:D.118, A:D.118 pi-Stacking: A:F.44 OCZ.7: 11 residues within 4Å: Chain B: I.41, F.79, A.83, L.86, Y.87, G.89, F.91, I.117, D.118, F.138 Ligands: OCZ.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.41, B:A.83, B:L.86, B:Y.87, B:I.117, B:D.118, B:F.138 Hydrogen bonds: B:G.89 OCZ.8: 14 residues within 4Å: Chain B: I.41, P.42, F.44, F.67, Q.115, N.116, I.117, D.118, H.135, I.180, V.181, F.182 Ligands: AR6.6, OCZ.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.41, B:F.44, B:F.44, B:I.117, B:I.117, B:I.117, B:H.135 Hydrogen bonds: B:Q.115, B:I.117, B:D.118, B:D.118, B:D.118 pi-Stacking: B:F.44

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 9 residues within 4Å: Chain B: T.37, G.40, I.41, P.42, D.43, S.46, T.49, K.235 Ligands: AR6.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.46, B:S.46, B:T.49 Water bridges: B:D.43

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

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