SMTL ID : 1s7g.1

Structural Basis for the Mechanism and Regulation of Sir2 Enzymes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.126, C.129, C.150, C.153 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.126, A:C.129, A:C.150, A:C.153 ZN.2: 4 residues within 4Å: Chain A: H.17, E.180, H.183 Chain C: H.130 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Metal complexes: C:H.130, A:H.17, A:E.180, A:E.180, A:H.183 ZN.10: 4 residues within 4Å: Chain B: C.126, C.129, C.150, C.153 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.126, B:C.129, B:C.150, B:C.153 ZN.11: 3 residues within 4Å: Chain B: H.17, E.180, H.183 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.17, B:E.180, B:H.183 ZN.20: 4 residues within 4Å: Chain C: C.126, C.129, C.150, C.153 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.126, C:C.129, C:C.150, C:C.153 ZN.21: 4 residues within 4Å: Chain A: H.130 Chain C: H.17, E.180, H.183 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.17, C:E.180, C:E.180, C:H.183, A:H.130 ZN.27: 4 residues within 4Å: Chain D: C.126, C.129, C.150, C.153 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.126, D:C.129, D:C.150, D:C.153 ZN.28: 3 residues within 4Å: Chain D: H.17, E.180, H.183 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.17, D:E.180, D:H.183 ZN.32: 4 residues within 4Å: Chain E: C.126, C.129, C.150, C.153 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.126, E:C.129, E:C.150, E:C.153

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

SO4.3: 8 residues within 4Å: Chain A: P.170, Q.171, R.172, T.173 Chain C: L.169, P.170, Q.171, R.172 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Q.171, C:Q.171, C:R.172, A:Q.171, A:R.172, A:T.173, A:T.173 SO4.4: 2 residues within 4Å: Chain A: K.123, R.161 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.123, A:R.161 SO4.5: 5 residues within 4Å: Chain A: E.87, M.91, K.247, R.250 Chain D: R.90 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:E.87, A:R.250 Salt bridges: A:K.247, D:R.90 SO4.6: 2 residues within 4Å: Chain A: K.57 Chain C: K.182 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Salt bridges: A:K.57, B:K.208, C:K.182 SO4.12: 4 residues within 4Å: Chain B: P.170, Q.171, R.172, T.173 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.171, B:R.172, B:T.173, B:T.173 Water bridges: B:R.172, B:R.172 Salt bridges: B:R.172 SO4.13: 3 residues within 4Å: Chain B: K.123, T.132, R.161 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.132 Salt bridges: B:K.123, B:R.161 SO4.14: 2 residues within 4Å: Chain B: R.6, K.7 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.6, B:K.7 SO4.15: 1 residues within 4Å: Chain B: R.149 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.149 SO4.22: 3 residues within 4Å: Chain C: K.123, T.132, R.161 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.132 Salt bridges: C:K.123, C:R.161 SO4.23: 1 residues within 4Å: Chain C: R.149 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.149 Salt bridges: C:R.149 SO4.29: 3 residues within 4Å: Chain D: K.123, T.132, R.161 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.123, D:R.161 SO4.30: 7 residues within 4Å: Chain D: G.23, A.24, G.25, Q.100, G.191, S.192, S.193 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.24, D:G.25, D:Q.100, D:S.193, D:S.193

3 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.7: 19 residues within 4Å: Chain A: G.23, A.24, G.25, A.28, E.29, T.34, F.35, Q.100, G.191, S.192, S.193, V.195, N.217, A.218, E.219, G.233, K.234, A.235 Chain B: P.220 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.195 Hydrogen bonds: A:A.24, A:G.25, A:E.29, A:F.35, A:Q.100, A:H.118, A:S.193, A:N.217, A:A.218, A:E.219, A:A.235 Water bridges: A:E.29, A:V.195, A:V.196 NAD.16: 27 residues within 4Å: Chain B: G.23, A.24, G.25, S.27, A.28, E.29, I.32, P.33, T.34, F.35, R.36, Q.100, N.101, I.102, D.103, H.118, G.191, S.192, S.193, V.196, N.217, A.218, E.219, G.233, K.234, A.235 Ligands: 2PE.17 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:A.24, B:I.32, B:F.35 Hydrogen bonds: B:A.24, B:S.27, B:E.29, B:F.35, B:R.36, B:R.36, B:Q.100, B:N.101, B:I.102, B:D.103, B:D.103, B:D.103, B:S.192, B:S.193, B:S.193, B:N.217, B:A.218, B:E.219, B:E.219, B:A.235 Water bridges: B:E.29, B:H.118 NAD.24: 27 residues within 4Å: Chain C: G.23, A.24, G.25, S.27, A.28, E.29, I.32, P.33, T.34, F.35, R.36, Q.100, N.101, I.102, D.103, H.118, G.191, S.192, S.193, V.196, N.217, A.218, E.219, G.233, K.234, A.235 Ligands: P6G.25 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:A.24, C:I.32, C:F.35 Hydrogen bonds: C:A.24, C:S.27, C:E.29, C:F.35, C:R.36, C:R.36, C:N.101, C:I.102, C:D.103, C:D.103, C:S.192, C:S.193, C:S.193, C:N.217, C:A.218, C:E.219, C:E.219, C:E.219, C:A.235 Water bridges: C:R.36, C:L.194, C:L.194

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 7 residues within 4Å: Chain A: F.63, S.67, K.73, L.74, I.102, M.121 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.67

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 2 residues within 4Å: Chain A: F.165 Ligands: 1PE.8 No protein-ligand interaction detected (PLIP) EDO.18: 1 residues within 4Å: Chain B: P.60 No protein-ligand interaction detected (PLIP) EDO.19: 6 residues within 4Å: Chain B: K.159, V.162, V.163, E.167, P.168, P.170 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.159, B:V.162, B:P.168

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.17: 18 residues within 4Å: Chain B: F.35, R.43, A.51, F.66, S.67, M.68, I.102, M.104, R.108, H.118, W.135, V.163, L.164, F.165, L.169, V.196, Y.197 Ligands: NAD.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.197 Water bridges: B:H.118

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.25: 9 residues within 4Å: Chain C: I.32, F.35, F.66, S.67, I.102, H.118, V.163, F.165 Ligands: NAD.24 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.43

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.26: 3 residues within 4Å: Chain C: P.60, R.61, Y.156 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.58, C:R.61 PG4.31: 9 residues within 4Å: Chain D: A.51, F.63, F.66, S.67, I.102, H.118, V.163, L.164, F.165 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.118

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

APR.33: 22 residues within 4Å: Chain E: G.23, A.24, G.25, A.28, E.29, T.34, F.35, R.36, W.42, Q.100, H.118, F.165, G.191, S.192, S.193, V.196, N.217, A.218, E.219, G.233, K.234, A.235 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:A.24, E:E.29, E:F.35, E:R.36, E:R.36, E:R.36, E:W.42, E:Q.100, E:Q.100, E:S.193, E:S.193, E:L.194, E:N.217, E:A.218, E:E.219, E:A.235 Water bridges: E:A.28 Salt bridges: E:R.36, E:R.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Avalos, J.L. et al., Structural basis for the mechanism and regulation of sir2 enzymes. Mol.Cell (2004)

Release Date

2004-03-23

Peptides

NAD-dependent deacetylase 2: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

NAD-dependent deacetylase 2

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