SMTL ID : 4rmj.1

Human Sirt2 in complex with ADP ribose and nicotinamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

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)

AR6.1: 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: EDO.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.33, A:T.37, A:T.37, A:F.44, A:R.45, A:Y.52, A:Y.52, 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 AR6.8: 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: EDO.10 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:A.33, 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:C.272 Water bridges: B:T.37, B:D.273 Salt bridges: B:R.45, B:R.45

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.2: 8 residues within 4Å: Chain A: I.41, P.42, F.44, L.51, L.86, N.116, I.117, D.118 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.86, A:I.117 Hydrogen bonds: A:I.117, A:D.118, A:D.118 pi-Stacking: A:F.44

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

PEG.3: 5 residues within 4Å: Chain A: M.3, E.4, P.225, L.226, S.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.4, A:L.226

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: F.67, H.135, V.181 Chain B: L.245 Ligands: AR6.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.135 EDO.9: 3 residues within 4Å: Chain B: A.267, W.268, L.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.269 EDO.10: 5 residues within 4Å: Chain A: L.245 Chain B: F.44, H.135, V.181 Ligands: AR6.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.181

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 7 residues within 4Å: Chain A: I.35, S.36, H.97, N.116, D.118, L.120, E.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.36, A:N.116, A:D.118

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 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.7: 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

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

PGE.11: 11 residues within 4Å: Chain B: Q.213, G.239, Q.240, S.241, F.244, M.247, I.248, M.249, G.250, G.252, G.254 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.213, B:Q.213, B:I.248, B:M.249, B:G.252 Water bridges: B:G.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rumpf, T. et al., Selective Sirt2 inhibition by ligand-induced rearrangement of the active site. Nat Commun (2015)

Release Date

2015-02-25

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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