SMTL ID : 3pki.7 (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

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

UNX.1: 2 residues within 4Å: Chain A: L.192, R.220 No protein-ligand interaction detected (PLIP) UNX.3: 1 residues within 4Å: Ligands: AR6.4 No protein-ligand interaction detected (PLIP) UNX.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain B: H.133 Ligands: UNX.16, UNX.18 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Chain B: L.192, I.219 Ligands: UNX.14 No protein-ligand interaction detected (PLIP) UNX.18: 4 residues within 4Å: Chain B: L.186, D.187 Ligands: UNX.14, UNX.19 No protein-ligand interaction detected (PLIP) UNX.19: 2 residues within 4Å: Chain B: W.188 Ligands: UNX.18 No protein-ligand interaction detected (PLIP) UNX.20: 2 residues within 4Å: Chain B: M.136, I.185 No protein-ligand interaction detected (PLIP) UNX.27: 1 residues within 4Å: Chain C: L.192 No protein-ligand interaction detected (PLIP) UNX.28: 2 residues within 4Å: Chain C: L.192, R.220 No protein-ligand interaction detected (PLIP) UNX.29: 4 residues within 4Å: Chain C: L.186, W.188 Ligands: UNX.30, UNX.33 No protein-ligand interaction detected (PLIP) UNX.30: 2 residues within 4Å: Ligands: UNX.29, UNX.31 No protein-ligand interaction detected (PLIP) UNX.31: 1 residues within 4Å: Ligands: UNX.30 No protein-ligand interaction detected (PLIP) UNX.32: 3 residues within 4Å: Chain C: H.133, I.219 Ligands: UNX.33 No protein-ligand interaction detected (PLIP) UNX.33: 3 residues within 4Å: Ligands: AR6.22, UNX.29, UNX.32 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.10: 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.21: 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)

AR6.4: 22 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 Ligands: UNX.3 20 PLIP interactions: 20 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:T.215, A:T.215, A:S.216, A:L.217, A:N.240, A:L.241, A:Q.242, A:Q.242, A:V.258 Water bridges: A:T.57 Salt bridges: A:R.65, A:R.65, A:R.65 AR6.11: 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 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:A.53, B:T.57, B:F.64, B:R.65, B:R.65, B:G.66, B:Q.113, B:H.133, B:T.215, B:S.216, B:N.240, B:L.241, B:Q.242, B:Q.242, B:V.258 Water bridges: B:E.22, B:T.57, B:D.259 Salt bridges: B:R.65, B:R.65 AR6.22: 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, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Ligands: UNX.33 19 PLIP interactions: 19 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:T.215, C:S.216, C:N.240, C:L.241, C:Q.242, C:Q.242, C:V.258 Water bridges: C:T.57, C:D.259 Salt bridges: C:R.65, C:R.65, C:R.65

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

SO4.5: 6 residues within 4Å: Chain A: V.153, V.154, G.155, T.162, R.164 Chain B: K.296 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.296, A:R.164 Hydrogen bonds: A:G.155 SO4.6: 5 residues within 4Å: Chain A: D.25, E.29, K.33, R.253, H.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.25 Salt bridges: A:K.33, A:R.253, A:H.255 SO4.7: 3 residues within 4Å: Chain A: P.67, H.68, R.76 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.68, A:R.76 SO4.8: 2 residues within 4Å: Chain A: H.68, K.81 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.81, A:D.83, A:D.83 Salt bridges: A:H.68 SO4.9: 3 residues within 4Å: Chain A: R.220, P.221, N.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.224 Salt bridges: A:R.220 SO4.13: 5 residues within 4Å: Chain B: V.154, G.155, T.162, R.164 Chain C: K.296 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.155 Salt bridges: B:R.164, C:K.296 SO4.15: 3 residues within 4Å: Chain B: H.68, K.81, D.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.81, B:K.81 Water bridges: B:H.68 Salt bridges: B:H.68 SO4.17: 4 residues within 4Å: Chain B: 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 SO4.23: 3 residues within 4Å: Chain C: R.90, A.275, W.276 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.276 Water bridges: C:R.90, C:R.90 Salt bridges: C:R.90 SO4.24: 6 residues within 4Å: Chain A: K.296 Chain C: V.153, V.154, G.155, T.162, R.164 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Salt bridges: A:K.296, C:R.164 Hydrogen bonds: C:G.155 SO4.25: 4 residues within 4Å: Chain C: K.245, H.246, R.248, H.249 4 PLIP interactions: 4 interactions with chain C Water bridges: C:D.247 Salt bridges: C:H.246, C:R.248, C:H.249 SO4.26: 2 residues within 4Å: Chain C: H.68, K.81 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.81 Salt bridges: C:H.68

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
A

B
B

C
C

NAD-dependent deacetylase sirtuin-6

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