SMTL ID : 5d7q.1

Crystal structure of human Sirt2 in complex with ADPR and CHIC35

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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: 4I5.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:A.33, A:T.37, A:T.37, A:F.44, A:R.45, A:R.45, A:Y.52, A:Q.115, A:Q.115, A:T.210, A:S.211, A:N.234, A:K.235, A:E.236, A:C.272 Water bridges: A:S.38, A:Q.213, A:D.273 Salt bridges: A:R.45, A:R.45 AR6.6: 23 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: 4I5.7 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:A.33, B:T.37, B:F.44, B:R.45, B:R.45, B:Y.52, B:Y.52, B:Q.115, B:H.135, B:S.211, B:N.234, B:K.235, B:E.236, B:E.236, B:E.271, B:E.271, B:C.272 Water bridges: B:T.37, B:D.273 Salt bridges: B:R.45, B:R.45

4 x 4I5: (6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide(Non-covalent)

4I5.3: 15 residues within 4Å: Chain A: A.33, 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, 4I5.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.33, A:I.41, A:F.44, A:I.117, A:I.117, A:H.135 Hydrogen bonds: A:Q.115, A:I.117, A:D.118, A:D.118, A:D.118 pi-Stacking: A:F.44 4I5.4: 11 residues within 4Å: Chain A: I.41, F.67, F.79, A.83, L.86, Y.87, G.89, F.91, D.118, F.138 Ligands: 4I5.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.41, A:I.41, A:A.83, A:F.91, A:D.118 Hydrogen bonds: A:G.89 4I5.7: 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, 4I5.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.41, B:F.44, B:I.117, B:I.117, B:H.135 Hydrogen bonds: B:Q.115, B:I.117, B:D.118, B:D.118 pi-Stacking: B:F.44 4I5.8: 11 residues within 4Å: Chain B: I.41, F.67, F.79, A.83, L.86, Y.87, G.89, F.91, D.118, F.138 Ligands: 4I5.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.41, B:I.41, B:A.83, B:L.86, B:D.118, B:F.138 Hydrogen bonds: B:G.89, B:G.89

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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