SMTL ID : 3zgv.1

Structure of human SIRT2 in complex with ADP-ribose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: C.164, S.166, C.169, H.171, C.190, D.192, C.193, S.195 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.164, A:C.169, A:C.190, A:C.193 ZN.7: 7 residues within 4Å: Chain B: C.164, C.169, H.171, C.190, D.192, C.193, S.195 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.164, B:C.169, B:C.190, B:C.193

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: F.65, F.88, I.138, H.156, I.201, V.202, F.203 Ligands: AR6.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.88 Hydrogen bonds: A:V.202 Salt bridges: A:H.156 ACT.4: 2 residues within 4Å: Chain A: W.289, L.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.290 ACT.5: 6 residues within 4Å: Chain A: R.66, E.85, F.204, Q.234, V.235, I.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.85 Salt bridges: A:R.66 ACT.6: 10 residues within 4Å: Chain A: G.260, Q.261, S.262, P.264, M.268, M.270, L.272, G.273, G.274, G.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.273, A:G.274, A:G.275 ACT.8: 8 residues within 4Å: Chain A: L.266 Chain B: F.65, F.88, I.138, H.156, I.201, V.202 Ligands: AR6.9 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.138 Salt bridges: B:H.156 ACT.10: 5 residues within 4Å: Chain A: G.267 Chain B: Y.83, E.85, F.204 Ligands: GOL.11 No protein-ligand interaction detected (PLIP)

2 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.3: 26 residues within 4Å: Chain A: G.53, A.54, G.55, T.58, S.59, D.64, F.65, R.66, S.67, Y.73, Q.136, H.156, F.204, G.230, T.231, S.232, L.233, V.235, N.255, K.256, E.257, G.291, E.292, C.293 Chain B: L.266 Ligands: ACT.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.54, A:F.65, A:R.66, A:S.67, A:Y.73, A:Q.136, A:Q.136, A:T.231, A:T.231, A:S.232, A:S.232, A:N.255, A:K.256, A:E.292, A:C.293 Water bridges: A:T.58, A:L.233, A:L.233, A:K.256, A:D.294 Salt bridges: A:R.66, A:R.66, A:R.66 AR6.9: 28 residues within 4Å: Chain A: L.266 Chain B: G.53, A.54, G.55, T.58, S.59, D.64, F.65, R.66, S.67, Y.73, F.88, Q.136, H.156, F.204, G.230, T.231, S.232, L.233, Q.234, V.235, N.255, K.256, E.257, G.291, E.292, C.293 Ligands: ACT.8 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:A.54, B:G.55, B:S.59, B:F.65, B:R.66, B:R.66, B:Y.73, B:Q.136, B:Q.136, B:T.231, B:S.232, B:S.232, B:N.255, B:K.256, B:E.257, B:E.257, B:E.292, B:C.293 Water bridges: B:T.58, B:S.59, B:S.67, B:L.233, B:K.256, B:E.257, B:D.294 Salt bridges: B:R.66, B:R.66

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 5 residues within 4Å: Chain A: Y.83 Chain B: Y.83, P.84, E.85 Ligands: ACT.10 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.85, B:E.85

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 13 residues within 4Å: Chain B: G.260, Q.261, S.262, D.263, P.264, M.268, M.270, G.271, L.272, G.273, G.274, G.275, M.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.273 Water bridges: B:G.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moniot, S. et al., Crystal Structure Analysis of Human Sirt2 and its Adp-Ribose Complex. J.Struct.Biol. (2013)

Release Date

2013-03-13

Peptides

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2