SMTL ID : 4y6q.1

Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.144, C.149, C.170, C.173 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.144, A:C.149, A:C.170, A:C.173 ZN.3: 4 residues within 4Å: Chain B: C.144, C.149, C.170, C.173 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.144, B:C.149, B:C.170, B:C.173 ZN.5: 4 residues within 4Å: Chain C: C.144, C.149, C.170, C.173 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.144, C:C.149, C:C.170, C:C.173 ZN.7: 4 residues within 4Å: Chain D: C.144, C.149, C.170, C.173 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.144, D:C.149, D:C.170, D:C.173

4 x OMR: [(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] tetradecanoate(Non-covalent)

OMR.2: 29 residues within 4Å: Chain A: G.33, A.34, G.35, T.38, D.44, F.45, R.46, Y.53, F.68, L.87, P.89, F.92, Q.116, I.118, H.136, F.139, I.181, F.184, G.210, T.211, S.212, V.215, N.235, K.236, E.237, G.259, E.260, C.261 Chain D: S.187 37 PLIP interactions: 36 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.45, A:F.68, A:F.68, A:F.68, A:L.87, A:F.92, A:I.118, A:I.118, A:F.139, A:I.181, A:F.184 Hydrogen bonds: A:A.34, A:G.35, A:T.38, A:F.45, A:R.46, A:R.46, A:Q.116, A:T.211, A:S.212, A:S.212, A:N.235, A:K.236, A:E.237, A:C.261, D:S.187 Water bridges: A:S.39, A:R.46, A:R.46, A:Q.116, A:Q.116, A:D.262 Salt bridges: A:R.46, A:R.46, A:H.136, A:H.136 pi-Cation interactions: A:K.236 OMR.4: 29 residues within 4Å: Chain B: G.33, A.34, G.35, T.38, D.44, F.45, R.46, S.47, Y.53, F.68, F.80, L.87, P.89, Q.116, I.118, H.136, F.139, I.181, F.184, G.210, T.211, S.212, V.215, N.235, K.236, E.237, G.259, E.260, C.261 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:F.45, B:F.68, B:F.68, B:F.80, B:L.87, B:L.87, B:I.118, B:F.139, B:I.181, B:F.184 Hydrogen bonds: B:A.34, B:G.35, B:T.38, B:F.45, B:R.46, B:R.46, B:Q.116, B:T.211, B:S.212, B:N.235, B:K.236, B:E.237, B:E.237, B:C.261 Water bridges: B:S.39, B:R.46, B:R.46, B:K.236, B:D.262 Salt bridges: B:R.46, B:R.46, B:H.136, B:H.136 pi-Cation interactions: B:K.236 OMR.6: 29 residues within 4Å: Chain C: G.33, A.34, G.35, T.38, D.44, F.45, R.46, S.47, Y.53, F.68, L.87, P.89, F.92, Q.116, I.118, H.136, F.139, I.181, F.184, G.210, T.211, S.212, V.215, N.235, K.236, E.237, G.259, E.260, C.261 32 PLIP interactions: 32 interactions with chain C Hydrophobic interactions: C:F.45, C:F.68, C:F.68, C:F.68, C:L.87, C:L.87, C:F.92, C:I.118, C:I.118, C:I.181, C:F.184 Hydrogen bonds: C:A.34, C:G.35, C:T.38, C:F.45, C:R.46, C:R.46, C:Y.53, C:Q.116, C:S.212, C:N.235, C:K.236, C:E.237, C:E.237, C:C.261 Water bridges: C:T.38, C:R.46, C:R.46, C:D.262 Salt bridges: C:R.46, C:R.46, C:H.136 OMR.8: 22 residues within 4Å: Chain D: G.33, A.34, G.35, T.38, D.44, R.46, F.68, L.87, Q.116, I.118, H.136, F.139, G.210, T.211, S.212, V.215, N.235, K.236, E.237, G.259, E.260, C.261 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:F.68, D:F.68, D:L.87, D:I.118, D:F.139 Hydrogen bonds: D:A.34, D:G.35, D:T.38, D:T.38, D:H.136, D:S.212, D:N.235, D:K.236, D:E.237, D:C.261 Salt bridges: D:R.46, D:R.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feldman, J.L. et al., Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation. Biochemistry (2015)

Release Date

2016-01-06

Peptides

NAD-dependent protein deacetylase sirtuin-2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NAD-dependent protein deacetylase sirtuin-2

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