SMTL ID : 1yc2.6 (9 other biounits)

Sir2Af2-NAD-ADPribose-nicotinamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

8 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 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Metal complexes: C:H.130, A:H.17, A:E.180, A:H.183 ZN.8: 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.9: 4 residues within 4Å: Chain B: H.17, E.180, H.183 Chain D: H.130 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Metal complexes: B:H.17, B:E.180, B:E.180, B:H.183, D:H.130 ZN.17: 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.18: 4 residues within 4Å: Chain A: H.130 Chain C: H.17, E.180, H.183 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.17, C:E.180, C:H.183, A:H.130 ZN.28: 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.29: 4 residues within 4Å: Chain B: H.130 Chain D: H.17, E.180, H.183 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.17, D:E.180, D:H.183, B:H.130

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

SO4.3: 2 residues within 4Å: Chain A: T.132, R.161 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.123, A:R.161 SO4.10: 2 residues within 4Å: Chain B: K.123, R.161 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.123, B:R.161 SO4.11: 3 residues within 4Å: Chain B: M.91, K.247, R.250 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.87, B:R.250 Salt bridges: B:K.247 SO4.19: 7 residues within 4Å: Chain A: P.170, Q.171, R.172 Chain C: P.170, Q.171, R.172, T.173 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.172, C:T.173, C:T.173, A:Q.171, A:Q.171, A:R.172 Water bridges: C:R.172, C:R.172 Salt bridges: C:R.172, A:R.172 SO4.20: 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 SO4.21: 2 residues within 4Å: Chain C: R.6, K.7 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.6, C:K.7 SO4.22: 1 residues within 4Å: Chain C: R.149 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.149 SO4.30: 7 residues within 4Å: Chain B: P.170, Q.171, R.172 Chain D: P.170, Q.171, R.172, T.173 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.172, D:T.173, D:T.173, B:Q.171, B:R.172 SO4.31: 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 SO4.32: 3 residues within 4Å: Chain B: K.57 Chain C: K.208 Chain D: K.182 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Salt bridges: C:K.208, D:K.182, B:K.57

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

NAD.4: 22 residues within 4Å: Chain A: G.23, A.24, G.25, A.28, E.29, T.34, F.35, R.36, E.38, Q.100, G.191, S.192, S.193, V.195, V.196, N.217, A.218, E.219, G.233, K.234, A.235 Ligands: PG4.6 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.195 Hydrogen bonds: A:A.24, A:E.29, A:F.35, A:R.36, A:R.36, A:E.38, A:S.193, A:S.193, A:S.193, A:S.193, A:A.218, A:E.219, A:E.219, A:E.219, A:A.235 NAD.12: 21 residues within 4Å: Chain B: G.23, A.24, G.25, A.28, E.29, T.34, F.35, R.36, E.38, Q.100, G.191, S.192, S.193, V.196, N.217, A.218, E.219, G.233, K.234, A.235 Chain C: P.220 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:A.24, B:G.25, B:E.29, B:F.35, B:R.36, B:R.36, B:Q.100, B:H.118, B:S.193, B:N.217, B:A.218, B:E.219, B:E.219, B:A.235 Water bridges: B:A.28, B:V.195, B:V.196 NAD.23: 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: 2PE.25 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:A.24, C:F.35 Hydrogen bonds: C:A.24, C:E.29, C:F.35, C:R.36, C:Q.100, C:Q.100, C:N.101, C:I.102, C:D.103, C:D.103, C:D.103, C:H.118, C:S.192, C:S.193, C:A.218, C:E.219, C:E.219, C:A.235 Water bridges: C:A.28, C:R.36 NAD.33: 26 residues within 4Å: Chain D: 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, N.217, A.218, E.219, G.233, K.234, A.235 Ligands: 2PE.34 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:A.24, D:F.35 Hydrogen bonds: D:A.24, D:G.25, D:S.27, D:E.29, D:F.35, D:R.36, D:R.36, D:Q.100, D:Q.100, D:N.101, D:I.102, D:D.103, D:D.103, D:S.192, D:S.193, D:S.193, D:N.217, D:A.218, D:E.219, D:A.235

3 x NCA: NICOTINAMIDE(Non-covalent)

NCA.5: 7 residues within 4Å: Chain A: A.24, P.33, T.34, F.35, N.101, I.102, D.103 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.27, A:I.102, A:D.103, A:D.103 pi-Stacking: A:F.35 NCA.13: 8 residues within 4Å: Chain B: A.24, S.27, P.33, F.35, N.101, I.102, D.103 Ligands: EDO.14 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.35 Hydrogen bonds: B:S.27, B:I.102, B:D.103, B:D.103, B:D.103 NCA.24: 6 residues within 4Å: Chain C: Q.171, L.174, Y.197 Chain D: Q.171, Y.197 Ligands: 2PE.34 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.171, C:Q.171 pi-Stacking: C:Y.197

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

PG4.6: 9 residues within 4Å: Chain A: F.35, A.51, F.63, S.67, H.118, V.163, F.165 Chain D: M.222 Ligands: NAD.4 No protein-ligand interaction detected (PLIP)

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 5 residues within 4Å: Chain A: I.32, K.71, D.72, M.121, W.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.72

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

EDO.14: 2 residues within 4Å: Chain B: I.32 Ligands: NCA.13 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain B: V.163, L.164 Ligands: EDO.16 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain B: F.63, S.67, M.121 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.67 EDO.26: 2 residues within 4Å: Chain C: R.61, Y.156 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.61 EDO.27: 7 residues within 4Å: Chain A: R.172 Chain C: K.159, R.161, V.162, V.163, E.167, P.168 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.167

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

2PE.25: 17 residues within 4Å: Chain C: F.35, R.43, F.66, S.67, M.68, M.70, I.102, D.103, M.104, H.118, M.121, V.163, F.165, L.169, V.196, Y.197 Ligands: NAD.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.197 Water bridges: C:R.43, C:S.67, C:H.118 2PE.34: 11 residues within 4Å: Chain D: I.32, F.66, S.67, I.102, H.118, V.163, F.165, L.169, Y.197 Ligands: NCA.24, NAD.33 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Avalos, J.L. et al., Mechanism of Sirtuin Inhibition by Nicotinamide: Altering the NAD(+) Cosubstrate Specificity of a Sir2 Enzyme. Mol.Cell (2005)

Release Date

2005-03-29

Peptides

NAD-dependent deacetylase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

NAD-dependent deacetylase 2

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