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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 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.6: 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 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: 23 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 Chain B: L.251, G.252 Ligands: BU3.5 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B 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, B:L.251, B:L.251 Hydrogen bonds: A:R.45 pi-Stacking: A:F.44, A:F.67, A:F.138 pi-Cation interactions: A:R.45 5GR.7: 23 residues within 4Å: Chain A: L.251, G.252 Chain B: 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: BU3.10 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.44, B:F.44, B:R.45, B:F.67, B:F.79, B:A.83, B:Y.87, B:Y.87, B:F.91, B:F.138, B:F.138, B:F.182, B:F.183, B:V.214, A:L.251, A:L.251 Hydrogen bonds: B:R.45 Water bridges: B:H.135, B:H.135 pi-Stacking: B:F.44, B:F.67, B:F.138 pi-Cation interactions: B:R.45

2 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 EDO.8: 5 residues within 4Å: Chain B: T.11, L.12, E.13, A.267, W.268 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.12, B:E.13 Water bridges: B:A.267, B:A.267

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

2 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 BU3.10: 11 residues within 4Å: Chain B: A.33, I.41, P.42, D.43, F.44, R.45, Q.115, N.116, I.117, D.118 Ligands: 5GR.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.33, B:I.41, B:I.117 Hydrogen bonds: B:R.45, B:R.45, B:N.116, B:I.117, B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NAD-dependent protein deacetylase sirtuin-2

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