SMTL ID : 3pki.8 (7 other biounits)

Human SIRT6 crystal structure in complex with ADP ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.141, C.144, C.166, C.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:C.166, A:C.177 ZN.9: 4 residues within 4Å: Chain B: C.141, C.144, C.166, C.177 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.141, B:C.144, B:C.166, B:C.177 ZN.19: 5 residues within 4Å: Chain C: C.141, C.144, T.146, C.166, C.177 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.141, C:C.144, C:C.166, C:C.177

3 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: 21 residues within 4Å: Chain A: G.52, A.53, G.54, T.57, D.63, F.64, R.65, W.71, Q.113, H.133, W.188, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:A.53, A:T.57, A:T.57, A:F.64, A:R.65, A:G.66, A:Q.113, A:S.216, A:N.240, A:L.241, A:Q.242, A:Q.242, A:V.258 Water bridges: A:E.22, A:T.57, A:D.259 Salt bridges: A:R.65, A:R.65, A:R.65 AR6.10: 21 residues within 4Å: Chain B: G.52, A.53, G.54, T.57, D.63, F.64, R.65, W.71, Q.113, H.133, W.188, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:A.53, B:T.57, B:T.57, B:D.63, B:F.64, B:R.65, B:R.65, B:Q.113, B:T.215, B:T.215, B:S.216, B:N.240, B:L.241, B:Q.242, B:Q.242, B:V.258 Water bridges: B:T.57 Salt bridges: B:R.65, B:R.65 AR6.20: 21 residues within 4Å: Chain C: G.52, A.53, G.54, T.57, D.63, F.64, R.65, W.71, Q.113, H.133, W.188, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:A.53, C:T.57, C:D.63, C:F.64, C:R.65, C:Q.113, C:H.133, C:S.216, C:N.240, C:L.241, C:Q.242, C:Q.242, C:V.258 Water bridges: C:A.58, C:D.259 Salt bridges: C:R.65, C:R.65, C:R.65

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: V.154, G.155, R.164 Chain C: K.296 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Salt bridges: C:K.296, A:R.164 Hydrogen bonds: A:G.155 SO4.4: 3 residues within 4Å: Chain A: K.33, R.253, H.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.29 Salt bridges: A:K.33, A:R.253, A:H.255 SO4.5: 3 residues within 4Å: Chain A: G.173, L.174, R.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.174, A:R.175 SO4.11: 5 residues within 4Å: Chain A: K.296 Chain B: V.153, V.154, G.155, R.164 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.155 Salt bridges: B:R.164, A:K.296 SO4.12: 3 residues within 4Å: Chain B: R.205, R.231, R.232 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.231, B:R.232 SO4.13: 3 residues within 4Å: Chain B: R.90, A.275, W.276 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.276 Water bridges: B:R.90, B:R.90, B:R.90, B:R.90, B:W.276 Salt bridges: B:R.90 SO4.14: 5 residues within 4Å: Chain B: D.25, E.29, K.33, R.253, H.255 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.33, B:R.253, B:H.255 SO4.15: 5 residues within 4Å: Chain B: K.296 Chain C: V.154, G.155, T.162, R.164 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:K.296, C:R.164 Hydrogen bonds: C:V.153, C:G.155 SO4.16: 3 residues within 4Å: Chain B: K.245, H.246, H.249 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.246, B:H.249 SO4.21: 3 residues within 4Å: Chain C: R.90, A.275, W.276 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.276 Water bridges: C:R.90 Salt bridges: C:R.90 SO4.22: 2 residues within 4Å: Chain A: R.172 Chain C: R.232 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.232

11 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.6: 1 residues within 4Å: Chain A: D.190 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: F.109, L.199 No protein-ligand interaction detected (PLIP) UNX.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.23: 2 residues within 4Å: Ligands: UNX.24, UNX.26 No protein-ligand interaction detected (PLIP) UNX.24: 4 residues within 4Å: Chain C: L.186, D.187 Ligands: UNX.23, UNX.25 No protein-ligand interaction detected (PLIP) UNX.25: 2 residues within 4Å: Chain C: W.188 Ligands: UNX.24 No protein-ligand interaction detected (PLIP) UNX.26: 5 residues within 4Å: Chain C: L.192, I.219, R.220 Ligands: UNX.23, UNX.27 No protein-ligand interaction detected (PLIP) UNX.27: 2 residues within 4Å: Chain C: D.190 Ligands: UNX.26 No protein-ligand interaction detected (PLIP) UNX.28: 2 residues within 4Å: Chain C: F.82, T.84 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, P.W. et al., Structure and biochemical functions of SIRT6. J.Biol.Chem. (2011)

Release Date

2011-01-26

Peptides

NAD-dependent deacetylase sirtuin-6: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

NAD-dependent deacetylase sirtuin-6

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