SMTL ID : 8zvp.1

Human SIRT6 in complex with EGCG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.132, C.135, C.157, C.168 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.132, A:C.157, A:C.168 ZN.4: 4 residues within 4Å: Chain B: C.132, C.135, C.157, C.168 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.132, B:C.135, B:C.157, B:C.168 ZN.6: 4 residues within 4Å: Chain C: C.132, C.135, C.157, C.168 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.132, C:C.157, C:C.168 ZN.9: 4 residues within 4Å: Chain D: C.132, C.135, C.157, C.168 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.132, D:C.135, D:C.157, D:C.168 ZN.11: 4 residues within 4Å: Chain E: C.132, C.135, C.157, C.168 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.132, E:C.157, E:C.168 ZN.14: 4 residues within 4Å: Chain F: C.132, C.135, C.157, C.168 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.132, F:C.135, F:C.157, F:C.168

6 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)

AR6.2: 23 residues within 4Å: Chain A: G.43, A.44, G.45, T.48, D.54, F.55, R.56, W.62, Q.104, H.124, W.179, G.205, T.206, S.207, I.210, N.231, L.232, Q.233, G.247, Y.248, V.249 Chain B: D.74 Ligands: KDH.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.44, A:T.48, A:T.48, A:F.55, A:R.56, A:T.206, A:T.206, A:S.207, A:L.208, A:N.231, A:L.232, A:Q.233, A:Q.233, A:V.249 Salt bridges: A:R.56, A:R.56, A:R.56 AR6.5: 21 residues within 4Å: Chain A: D.74 Chain B: G.43, A.44, G.45, T.48, D.54, F.55, R.56, W.62, Q.104, H.124, G.205, T.206, S.207, I.210, N.231, L.232, Q.233, G.247, Y.248, V.249 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:A.44, B:T.48, B:T.48, B:F.55, B:R.56, B:R.56, B:H.124, B:T.206, B:S.207, B:S.207, B:N.231, B:L.232, B:Q.233, B:Q.233, B:V.249 Salt bridges: B:R.56, B:R.56 AR6.7: 23 residues within 4Å: Chain C: G.43, A.44, G.45, T.48, D.54, F.55, R.56, W.62, Q.104, H.124, W.179, G.205, T.206, S.207, I.210, N.231, L.232, Q.233, G.247, Y.248, V.249 Chain D: D.74 Ligands: KDH.8 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:A.44, C:T.48, C:T.48, C:F.55, C:R.56, C:T.206, C:T.206, C:S.207, C:L.208, C:N.231, C:L.232, C:Q.233, C:Q.233, C:V.249 Salt bridges: C:R.56, C:R.56, C:R.56 AR6.10: 21 residues within 4Å: Chain C: D.74 Chain D: G.43, A.44, G.45, T.48, D.54, F.55, R.56, W.62, Q.104, H.124, G.205, T.206, S.207, I.210, N.231, L.232, Q.233, G.247, Y.248, V.249 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:A.44, D:T.48, D:T.48, D:F.55, D:R.56, D:R.56, D:H.124, D:T.206, D:S.207, D:S.207, D:N.231, D:L.232, D:Q.233, D:Q.233, D:V.249 Salt bridges: D:R.56, D:R.56 AR6.12: 23 residues within 4Å: Chain E: G.43, A.44, G.45, T.48, D.54, F.55, R.56, W.62, Q.104, H.124, W.179, G.205, T.206, S.207, I.210, N.231, L.232, Q.233, G.247, Y.248, V.249 Chain F: D.74 Ligands: KDH.13 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:A.44, E:T.48, E:T.48, E:F.55, E:R.56, E:T.206, E:T.206, E:S.207, E:L.208, E:N.231, E:L.232, E:Q.233, E:Q.233, E:V.249 Salt bridges: E:R.56, E:R.56, E:R.56 AR6.15: 21 residues within 4Å: Chain E: D.74 Chain F: G.43, A.44, G.45, T.48, D.54, F.55, R.56, W.62, Q.104, H.124, G.205, T.206, S.207, I.210, N.231, L.232, Q.233, G.247, Y.248, V.249 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:A.44, F:T.48, F:T.48, F:F.55, F:R.56, F:R.56, F:H.124, F:T.206, F:S.207, F:S.207, F:N.231, F:L.232, F:Q.233, F:Q.233, F:V.249 Salt bridges: F:R.56, F:R.56

3 x KDH: (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate(Non-covalent)

KDH.3: 15 residues within 4Å: Chain A: I.52, P.53, D.54, F.55, V.61, W.62, F.73, F.77, V.106, M.127, M.148, I.176, L.177, W.179 Ligands: AR6.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.52, A:V.61, A:F.73, A:F.77, A:V.106 Hydrogen bonds: A:L.177 KDH.8: 15 residues within 4Å: Chain C: I.52, P.53, D.54, F.55, V.61, W.62, F.73, F.77, V.106, M.127, M.148, I.176, L.177, W.179 Ligands: AR6.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.52, C:V.61, C:F.73, C:F.77, C:V.106 Hydrogen bonds: C:L.177 KDH.13: 15 residues within 4Å: Chain E: I.52, P.53, D.54, F.55, V.61, W.62, F.73, F.77, V.106, M.127, M.148, I.176, L.177, W.179 Ligands: AR6.12 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:I.52, E:V.61, E:F.73, E:F.77, E:V.106 Hydrogen bonds: E:L.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, B. et al., SIRT6 in complex with EGCG. To Be Published

Release Date

2025-06-18

Peptides

NAD-dependent protein deacylase sirtuin-6: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

NAD-dependent protein deacylase sirtuin-6