SMTL ID : 5dy5.2 (1 other biounit)

Crystal structure of human Sirt2 in complex with a SirReal probe fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 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

1 x 5GR: N-(5-{3-[(1-benzyl-1H-1,2,3-triazol-4-yl)methoxy]benzyl}-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide(Non-covalent)

5GR.2: 21 residues within 4Å: Chain A: I.41, F.44, R.45, I.66, F.67, F.79, A.83, L.86, Y.87, P.88, F.91, I.117, D.118, H.135, F.138, I.180, V.181, F.182, F.183, V.214 Ligands: BU3.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.44, A:F.44, A:R.45, A:F.67, A:F.79, A:A.83, A:Y.87, A:Y.87, A:F.91, A:F.138, A:F.138, A:F.182, A:F.183, A:V.214 Hydrogen bonds: A:R.45 pi-Stacking: A:F.44, A:F.67, A:F.138 pi-Cation interactions: A:R.45

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

EDO.3: 5 residues within 4Å: Chain A: T.11, L.12, E.13, A.267, W.268 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.12, A:E.13 Water bridges: A:A.267, A:A.267

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 4 residues within 4Å: Chain A: E.9, T.11, E.13, R.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.11 Water bridges: A:R.17 Salt bridges: A:E.9, A:E.9, A:R.17

1 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.5: 11 residues within 4Å: Chain A: A.33, I.41, P.42, D.43, F.44, R.45, Q.115, N.116, I.117, D.118 Ligands: 5GR.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.33, A:I.41, A:I.117 Hydrogen bonds: A:R.45, A:R.45, A:N.116, A:I.117, A:D.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiedel, M. et al., Structure-Based Development of an Affinity Probe for Sirtuin 2. Angew.Chem.Int.Ed.Engl. (2016)

Release Date

2016-01-20

Peptides

NAD-dependent protein deacetylase sirtuin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-2

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