SMTL ID : 3pkj.7 (6 other biounits)

Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-hexamer

Ligands

6 x A2N: [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate(Non-covalent)

A2N.1: 23 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, L.186, W.188, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Chain F: D.83 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:H.133 Hydrogen bonds: A:A.53, A:T.57, A:T.57, A:D.63, A:F.64, A:R.65, A:R.65, A:W.71, A:Q.113, A:H.133, A:T.215, A:T.215, A:S.216, A:S.216, A:L.217, A:N.240, A:L.241, A:Q.242, A:Q.242, A:V.258 Water bridges: A:Q.218, A:D.259 Salt bridges: A:R.65, A:R.65 A2N.16: 23 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, L.186, W.188, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Chain E: D.83 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:H.133 Hydrogen bonds: B:A.53, B:T.57, B:T.57, B:F.64, B:R.65, B:R.65, B:G.66, B:W.71, B:Q.113, B:H.133, B:T.215, B:S.216, B:S.216, B:L.217, B:N.240, B:L.241, B:Q.242, B:Q.242, B:V.258 Salt bridges: B:R.65, B:R.65 A2N.22: 22 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, L.186, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Chain D: D.83 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:A.53, C:G.54, C:T.57, C:F.64, C:R.65, C:W.71, C:Q.113, C:H.133, C:T.215, C:S.216, C:S.216, C:L.217, C:N.240, C:L.241, C:Q.242, C:Q.242, C:V.258 Water bridges: C:T.57, C:Q.218 A2N.32: 21 residues within 4Å: Chain C: D.83 Chain D: G.52, A.53, G.54, T.57, D.63, F.64, R.65, W.71, Q.113, H.133, L.186, G.214, T.215, S.216, N.240, L.241, Q.242, G.256, Y.257, V.258 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:A.53, D:G.54, D:T.57, D:F.64, D:R.65, D:Q.113, D:H.133, D:T.215, D:S.216, D:S.216, D:L.217, D:N.240, D:L.241, D:Q.242, D:Q.242, D:V.258 Water bridges: D:A.58 A2N.41: 23 residues within 4Å: Chain B: D.83 Chain E: G.52, A.53, G.54, T.57, D.63, F.64, R.65, W.71, Q.113, H.133, L.186, W.188, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 25 PLIP interactions: 25 interactions with chain E Hydrogen bonds: E:A.53, E:G.54, E:T.57, E:D.63, E:F.64, E:R.65, E:R.65, E:G.66, E:Q.113, E:H.133, E:T.215, E:T.215, E:S.216, E:S.216, E:L.217, E:N.240, E:L.241, E:Q.242, E:Q.242, E:V.258 Water bridges: E:T.57, E:Q.218, E:D.259 Salt bridges: E:R.65, E:R.65 A2N.47: 20 residues within 4Å: Chain A: D.83 Chain F: 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, N.240, L.241, Q.242, G.256, Y.257, V.258 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:A.53, F:T.57, F:T.57, F:F.64, F:R.65, F:W.71, F:Q.113, F:H.133, F:T.215, F:T.215, F:S.216, F:S.216, F:L.217, F:N.240, F:L.241, F:Q.242, F:Q.242, F:V.258 Salt bridges: F:R.65, F:R.65

6 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.17: 4 residues within 4Å: Chain B: C.141, C.144, C.166, R.178 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.141, B:C.144, B:C.166, B:R.178 ZN.23: 4 residues within 4Å: Chain C: C.141, C.144, 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 ZN.33: 4 residues within 4Å: Chain D: C.141, C.144, C.166, C.177 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.141, D:C.144, D:C.166, D:C.177 ZN.42: 4 residues within 4Å: Chain E: C.141, C.144, C.166, C.177 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.141, E:C.144, E:C.166, E:C.177 ZN.48: 4 residues within 4Å: Chain F: C.141, C.144, C.166, C.177 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.141, F:C.144, F:C.166, F:C.177

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

SO4.3: 4 residues within 4Å: Chain A: R.220, P.221, N.224 Ligands: UNX.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.224 SO4.18: 5 residues within 4Å: Chain B: H.68, K.81 Chain E: H.68, K.81, D.83 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Water bridges: B:H.68, E:H.68 Salt bridges: B:H.68, E:H.68 SO4.24: 5 residues within 4Å: Chain C: P.67, H.68, R.76 Chain D: L.78, A.79 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Salt bridges: C:H.68, C:R.76 Hydrogen bonds: D:A.79 SO4.25: 3 residues within 4Å: Chain C: K.33, R.253, H.255 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.33, C:H.255 SO4.26: 2 residues within 4Å: Chain C: R.231, R.232 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.231, C:R.232 SO4.34: 6 residues within 4Å: Chain C: H.68, K.81, D.83 Chain D: H.68, K.81, D.83 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Water bridges: D:K.81, D:D.83 Salt bridges: D:H.68, C:H.68 SO4.35: 4 residues within 4Å: Chain D: E.29, K.33, R.253, H.255 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.33, D:H.255 SO4.36: 2 residues within 4Å: Chain D: R.164 Chain E: K.296 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.164 Salt bridges: D:R.164 SO4.43: 3 residues within 4Å: Chain E: K.33, R.253, H.255 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:K.33, E:H.255 SO4.49: 5 residues within 4Å: Chain F: T.85, F.86, E.87, V.153 Ligands: UNX.10 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:F.86, F:E.87 SO4.50: 3 residues within 4Å: Chain F: V.153, G.155, R.164 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.155 Salt bridges: F:R.164 SO4.51: 4 residues within 4Å: Chain A: H.68, K.81 Chain F: H.68, K.81 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F Water bridges: A:D.83, A:D.83 Salt bridges: A:H.68, F:H.68

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

UNX.4: 2 residues within 4Å: Chain A: G.77, L.78 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: A.161 Ligands: UNX.8 Ligand excluded by PLIP UNX.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.7: 5 residues within 4Å: Chain A: V.281 Chain B: R.291, P.292, P.293, T.294 Ligand excluded by PLIP UNX.8: 1 residues within 4Å: Ligands: UNX.5 Ligand excluded by PLIP UNX.9: 1 residues within 4Å: Chain A: R.195 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain A: Y.257 Ligands: SO4.49 Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain B: T.294 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: F.24, D.25, P.26 Ligand excluded by PLIP UNX.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.14: 1 residues within 4Å: Chain A: A.169 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: N.224 Ligands: SO4.3 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain B: E.131, Q.147, D.196 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain B: E.202, N.206 Ligand excluded by PLIP UNX.21: 1 residues within 4Å: Chain B: F.24 Ligand excluded by PLIP UNX.27: 1 residues within 4Å: Chain C: P.21 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain C: R.103, L.286, L.289 Ligand excluded by PLIP UNX.29: 1 residues within 4Å: Chain C: R.103 Ligand excluded by PLIP UNX.30: 1 residues within 4Å: Chain C: Q.43 Ligand excluded by PLIP UNX.31: 1 residues within 4Å: Chain C: R.164 Ligand excluded by PLIP UNX.37: 1 residues within 4Å: Chain D: D.127 Ligand excluded by PLIP UNX.38: 2 residues within 4Å: Chain D: W.42 Chain F: Y.148 Ligand excluded by PLIP UNX.39: 6 residues within 4Å: Chain D: N.114, D.116, G.117, L.118, H.119, E.131 Ligand excluded by PLIP UNX.40: 1 residues within 4Å: Chain D: A.13 Ligand excluded by PLIP UNX.44: 2 residues within 4Å: Chain E: V.281, E.283 Ligand excluded by PLIP UNX.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.46: 3 residues within 4Å: Chain E: E.102, G.105, P.288 Ligand excluded by PLIP UNX.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.53: 3 residues within 4Å: Chain D: P.292, P.293 Chain F: D.151 Ligand excluded by PLIP UNX.54: 1 residues within 4Å: Chain F: D.251 Ligand excluded by PLIP UNX.55: 1 residues within 4Å: Chain F: R.164 Ligand excluded by PLIP UNX.56: 3 residues within 4Å: Chain F: F.109, E.202, A.203 Ligand excluded by PLIP UNX.57: 3 residues within 4Å: Chain F: E.140, P.193, D.196 Ligand excluded by PLIP UNX.58: 2 residues within 4Å: Chain F: E.180 Ligands: UNX.59 Ligand excluded by PLIP UNX.59: 1 residues within 4Å: Ligands: UNX.58 Ligand excluded by 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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
B

D
E

E
A

F
F

NAD-dependent deacetylase sirtuin-6

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