SMTL ID : 3k35.7 (6 other biounits)

Crystal Structure of Human SIRT6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 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.8: 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.17: 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 ZN.23: 5 residues within 4Å: Chain D: C.141, C.144, T.146, 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.30: 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.37: 5 residues within 4Å: Chain F: C.141, C.144, T.146, 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

6 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.2: 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, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Chain B: D.83 Ligands: UNX.5 17 PLIP interactions: 17 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 Salt bridges: A:R.65, A:R.65, A:R.65 APR.9: 22 residues within 4Å: Chain A: D.83 Chain B: 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.16 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.53, B:G.54, B:T.57, B:T.57, B:F.64, B:R.65, B:R.65, B:W.71, B:H.133, B:S.216, B:S.216, B:N.240, B:L.241, B:Q.242, B:Q.242, B:V.258 Water bridges: B:A.58, B:Q.113, B:D.259, A:K.81 Salt bridges: B:R.65, B:R.65 APR.18: 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, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Chain F: D.83 Ligands: UNX.21 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:A.53, C:T.57, C:T.57, C:D.63, C:F.64, C:R.65, C:R.65, C:W.71, 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:Q.113, C:D.259, F:K.81 Salt bridges: C:R.65, C:R.65 APR.24: 22 residues within 4Å: Chain D: 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 Chain E: D.83 Ligands: UNX.28 20 PLIP interactions: 1 interactions with chain E, 19 interactions with chain D Water bridges: E:K.81, D:T.57, D:Q.113, D:D.259 Hydrogen bonds: D:A.53, D:G.54, D:T.57, D:F.64, D:R.65, D:R.65, D:W.71, D:H.133, D:S.216, D:N.240, D:L.241, D:Q.242, D:Q.242, D:V.258 Salt bridges: D:R.65, D:R.65 APR.31: 23 residues within 4Å: Chain D: D.83 Chain E: 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.35, UNX.36 22 PLIP interactions: 21 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:A.53, E:G.54, E:T.57, E:D.63, E:F.64, E:R.65, E:R.65, E:H.133, E:T.215, 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.113, E:D.259, D:K.81 Salt bridges: E:R.65, E:R.65 APR.38: 22 residues within 4Å: Chain C: 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, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Ligands: UNX.41 22 PLIP interactions: 22 interactions with chain F Hydrogen bonds: F:A.53, F:G.54, F:T.57, F:T.57, F:D.63, F:F.64, F:R.65, F:R.65, F:Q.113, F:T.215, F:S.216, F:N.240, F:L.241, F:Q.242, F:Q.242, F:V.258 Water bridges: F:E.22, F:L.217, F:Q.218, F:D.259 Salt bridges: F:R.65, F:R.65

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

SO4.3: 3 residues within 4Å: Chain A: K.33, R.253, H.255 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.33, A:R.253, A:H.255 SO4.4: 5 residues within 4Å: Chain A: V.153, V.154, G.155, R.164 Chain E: K.296 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.155, A:T.162 Salt bridges: A:R.164, E:K.296 SO4.10: 3 residues within 4Å: Chain B: 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 SO4.11: 6 residues within 4Å: Chain A: M.73, L.78, A.79 Chain B: P.67, H.68, R.76 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:R.76 Salt bridges: B:H.68, B:R.76 Hydrogen bonds: A:A.79, A:A.79 SO4.12: 4 residues within 4Å: Chain A: H.68, K.81 Chain B: H.68, K.81 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.81, B:K.81 Water bridges: A:K.81, B:K.81 Salt bridges: A:H.68, B:H.68 SO4.13: 3 residues within 4Å: Chain B: R.205, R.231, R.232 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.205 Salt bridges: B:R.205, B:R.231, B:R.232 SO4.19: 3 residues within 4Å: Chain C: R.220, P.221, N.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.224 Salt bridges: C:R.220 SO4.25: 5 residues within 4Å: Chain D: H.68, K.81, D.83 Chain E: H.68, K.81 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Salt bridges: E:H.68, D:H.68 Water bridges: D:K.81 SO4.26: 5 residues within 4Å: Chain D: P.67, H.68 Chain E: M.73, L.78, A.79 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Salt bridges: D:H.68 Hydrogen bonds: E:A.79, E:A.79 SO4.32: 4 residues within 4Å: Chain E: E.29, K.33, R.253, H.255 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:K.33, E:R.253, E:H.255 SO4.33: 5 residues within 4Å: Chain E: V.154, G.155, T.162, R.164 Chain F: K.296 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.155 Salt bridges: E:R.164, F:K.296 SO4.39: 4 residues within 4Å: Chain F: E.29, K.33, R.253, H.255 7 PLIP interactions: 7 interactions with chain F Water bridges: F:K.33, F:K.33, F:H.255, F:H.255 Salt bridges: F:K.33, F:R.253, F:H.255 SO4.40: 4 residues within 4Å: Chain C: H.68, K.81 Chain F: H.68, K.81 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain C Water bridges: F:H.68, F:K.81, F:D.83, C:H.68, C:K.81, C:D.83 Salt bridges: F:H.68, C:H.68

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

UNX.5: 2 residues within 4Å: Ligands: APR.2, UNX.6 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Ligands: UNX.5, UNX.7 Ligand excluded by PLIP UNX.7: 1 residues within 4Å: Ligands: UNX.6 Ligand excluded by PLIP UNX.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Ligands: UNX.16 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Ligands: APR.9, UNX.15 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain C: L.192 Ligands: UNX.21 Ligand excluded by PLIP UNX.21: 3 residues within 4Å: Ligands: APR.18, UNX.20, UNX.22 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain C: W.188 Ligands: UNX.21 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain D: H.133, I.219 Ligands: UNX.28 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Ligands: APR.24, UNX.27, UNX.29 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain D: W.188 Ligands: UNX.28 Ligand excluded by PLIP UNX.34: 4 residues within 4Å: Chain E: H.133, L.192, I.219 Ligands: UNX.35 Ligand excluded by PLIP UNX.35: 3 residues within 4Å: Ligands: APR.31, UNX.34, UNX.36 Ligand excluded by PLIP UNX.36: 3 residues within 4Å: Chain E: L.186 Ligands: APR.31, UNX.35 Ligand excluded by PLIP UNX.41: 2 residues within 4Å: Ligands: APR.38, UNX.42 Ligand excluded by PLIP UNX.42: 2 residues within 4Å: Chain F: L.192 Ligands: UNX.41 Ligand excluded by PLIP UNX.43: 0 residues within 4Å: (No contacts) 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

2009-12-08

Peptides

NAD-dependent deacetylase sirtuin-6: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
A

C
C

D
E

E
B

F
D

NAD-dependent deacetylase sirtuin-6

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