SMTL ID : 4rmg.2 (1 other biounit)

Human Sirt2 in complex with SirReal2 and NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 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.4: 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 3TE: 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide(Non-covalent)

3TE.2: 18 residues within 4Å: Chain A: I.41, F.44, I.66, F.67, F.79, A.83, L.86, Y.87, P.88, F.91, I.117, D.118, F.138, I.180, V.181, F.182 Chain B: M.247 Ligands: NAD.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.67, A:F.67, A:F.79, A:F.79, A:A.83, A:Y.87, A:Y.87, A:F.91, A:I.117, A:F.138, A:F.138, A:I.180, A:I.180 pi-Stacking: A:F.138, A:F.182 3TE.5: 18 residues within 4Å: Chain A: M.247 Chain B: I.41, F.44, I.66, F.67, F.79, A.83, L.86, Y.87, P.88, F.91, I.117, D.118, F.138, I.180, V.181, F.182 Ligands: NAD.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.79, B:F.79, B:A.83, B:Y.87, B:Y.87, B:F.91, B:I.117, B:F.138, B:F.138, B:I.180, B:I.180 pi-Stacking: B:F.138, B:F.182

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 26 residues within 4Å: Chain A: G.32, A.33, G.34, S.36, T.37, I.41, P.42, D.43, F.44, Q.115, N.116, I.117, D.118, H.135, G.209, T.210, S.211, N.234, K.235, E.236, G.270, E.271, C.272 Chain B: G.246, M.247 Ligands: 3TE.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:A.33, A:F.44 Hydrogen bonds: A:A.33, A:G.34, A:S.36, A:T.37, A:Q.115, A:Q.115, A:I.117, A:D.118, A:D.118, A:D.118, A:H.135, A:T.210, A:S.211, A:S.211, A:N.234, A:K.235, A:C.272 Water bridges: A:T.37, A:L.212, A:L.212, A:D.273 NAD.6: 26 residues within 4Å: Chain A: G.246, M.247 Chain B: G.32, A.33, G.34, S.36, T.37, I.41, P.42, D.43, F.44, Q.115, N.116, I.117, D.118, H.135, G.209, T.210, S.211, N.234, K.235, E.236, G.270, E.271, C.272 Ligands: 3TE.5 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:A.33, B:F.44 Hydrogen bonds: B:A.33, B:G.34, B:S.36, B:T.37, B:T.37, B:D.43, B:Q.115, B:Q.115, B:I.117, B:D.118, B:D.118, B:T.210, B:T.210, B:S.211, B:S.211, B:N.234, B:K.235, B:E.271, B:C.272 Water bridges: B:T.37, B:L.212, B:L.212, B:D.273

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
A

NAD-dependent protein deacetylase sirtuin-2

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