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

SIRT1/Activator/Substrate Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-dimer

Ligands

2 x ARG- HIS- LYS- ALY- LEU- NLE- PHE: Ac-p53(Non-covalent)

ARG-HIS-LYS-ALY-LEU-NLE-PHE.1: 18 residues within 4Å: Chain A: Q.112, F.115, H.181, I.229, V.230, F.231, F.232, G.233, E.234, N.235, L.236, H.241, K.262, V.263, R.264, P.265 Chain B: E.118 Ligands: CNA.3 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.115, A:H.181, A:I.229, A:F.232, A:L.236, A:P.265 Hydrogen bonds: A:V.230, A:G.233, A:E.234, A:K.262, A:R.264, A:R.264, B:E.118 pi-Cation interactions: A:H.241, A:R.264 ARG-HIS-LYS-ALY-LEU-NLE-PHE.7: 18 residues within 4Å: Chain A: E.118 Chain B: Q.112, F.115, H.181, I.229, V.230, F.231, F.232, G.233, E.234, N.235, L.236, H.241, K.262, V.263, R.264, P.265 Ligands: CNA.9 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.115, B:H.181, B:I.229, B:F.232, B:L.236, B:P.265 Hydrogen bonds: B:V.230, B:G.233, B:E.234, B:K.262, B:R.264, B:R.264, A:E.118 pi-Cation interactions: B:H.241, B:R.264

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.189, C.192, C.213, C.216 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.189, A:C.192, A:C.213, A:C.216 ZN.8: 4 residues within 4Å: Chain B: C.189, C.192, C.213, C.216 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.189, B:C.192, B:C.213, B:C.216

2 x CNA: CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

CNA.3: 27 residues within 4Å: Chain A: G.79, A.80, G.81, V.84, I.88, P.89, D.90, F.91, R.92, S.93, F.115, I.134, Q.163, N.164, I.165, D.166, G.258, S.259, S.260, L.261, N.283, R.284, E.285, G.298, D.299, C.300 Ligands: ARG-HIS-LYS-ALY-LEU-NLE-PHE.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:A.80, A:I.88, A:F.91, A:I.134 Hydrogen bonds: A:A.80, A:G.81, A:F.91, A:R.92, A:I.165, A:D.166, A:D.166, A:S.259, A:S.260, A:S.260, A:L.261, A:N.283, A:R.284, A:R.284, A:E.285, A:E.285, A:E.285, A:C.300 Water bridges: A:K.262, A:K.262 pi-Stacking: A:F.91 CNA.9: 27 residues within 4Å: Chain B: G.79, A.80, G.81, V.84, I.88, P.89, D.90, F.91, R.92, S.93, F.115, I.134, Q.163, N.164, I.165, D.166, G.258, S.259, S.260, L.261, N.283, R.284, E.285, G.298, D.299, C.300 Ligands: ARG-HIS-LYS-ALY-LEU-NLE-PHE.7 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:A.80, B:I.88, B:F.91, B:I.134 Hydrogen bonds: B:A.80, B:G.81, B:F.91, B:R.92, B:I.165, B:D.166, B:D.166, B:S.259, B:S.260, B:S.260, B:L.261, B:N.283, B:R.284, B:R.284, B:E.285, B:E.285, B:E.285, B:C.300 Water bridges: B:K.262, B:K.262 pi-Stacking: B:F.91

2 x 4TQ: (3S)-1,3-dimethyl-N-[3-(1,3-oxazol-5-yl)phenyl]-6-[3-(trifluoromethyl)phenyl]-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide(Non-covalent)

4TQ.4: 14 residues within 4Å: Chain A: L.24, T.27, P.29, P.30, T.37, Q.40, I.41, N.44, I.45, E.48 Chain B: L.24, T.27, E.48 Ligands: 4TQ.10 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.37, A:Q.40, A:I.41, A:I.41, A:I.45, B:L.24 Hydrogen bonds: A:N.44 4TQ.10: 14 residues within 4Å: Chain A: L.24, T.27, E.48 Chain B: L.24, T.27, P.29, P.30, T.37, Q.40, I.41, N.44, I.45, E.48 Ligands: 4TQ.4 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.37, B:Q.40, B:I.41, B:I.41, B:I.45, A:L.24 Hydrogen bonds: B:N.44

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: A.200, V.201, D.204, P.211, R.212, P.214, M.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.200, A:D.204 Water bridges: A:D.204 GOL.6: 5 residues within 4Å: Chain A: F.240, H.241, P.265, L.268, S.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.241, A:S.272 GOL.11: 7 residues within 4Å: Chain B: A.200, V.201, D.204, P.211, R.212, P.214, M.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.200, B:D.204 Water bridges: B:D.204 GOL.12: 5 residues within 4Å: Chain B: F.240, H.241, P.265, L.268, S.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.241, B:S.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, H. et al., Crystallographic structure of a small molecule SIRT1 activator-enzyme complex. Nat Commun (2015)

Release Date

2015-07-15

Peptides

NAD-dependent protein deacetylase sirtuin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NAD-dependent protein deacetylase sirtuin-1

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