SMTL ID : 1yc2.8 (9 other biounits)

Sir2Af2-NAD-ADPribose-nicotinamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 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 B: H.130 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.17, A:E.180, A:H.183, B:H.130 ZN.12: 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.13: 4 residues within 4Å: Chain A: H.130 Chain B: H.17, E.180, H.183 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.17, B:E.180, B:H.183, A:H.130

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

SO4.3: 7 residues within 4Å: Chain A: P.170, Q.171, R.172, T.173 Chain B: P.170, Q.171, R.172 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.172, A:T.173, A:T.173, B:Q.171, B:Q.171, B:R.172 Water bridges: A:R.172, A:R.172 Salt bridges: A:R.172, B:R.172 SO4.4: 3 residues within 4Å: Chain A: K.123, T.132, R.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.132 Salt bridges: A:K.123, A:R.161 SO4.5: 2 residues within 4Å: Chain A: R.6, K.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.6, A:K.7 SO4.6: 1 residues within 4Å: Chain A: R.149 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.149 SO4.14: 2 residues within 4Å: Chain B: T.132, R.161 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.123, B:R.161

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

NAD.7: 27 residues within 4Å: Chain A: 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.9 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.24, A:F.35 Hydrogen bonds: A:A.24, A:E.29, A:F.35, A:R.36, A:Q.100, A:Q.100, A:N.101, A:I.102, A:D.103, A:D.103, A:D.103, A:H.118, A:S.192, A:S.193, A:A.218, A:E.219, A:E.219, A:A.235 Water bridges: A:A.28, A:R.36 NAD.15: 22 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.195, V.196, N.217, A.218, E.219, G.233, K.234, A.235 Ligands: PG4.17 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.195 Hydrogen bonds: B:A.24, B:E.29, B:F.35, B:R.36, B:R.36, B:E.38, B:S.193, B:S.193, B:S.193, B:S.193, B:A.218, B:E.219, B:E.219, B:E.219, B:A.235

2 x NCA: NICOTINAMIDE(Non-covalent)

NCA.8: 3 residues within 4Å: Chain A: Q.171, L.174, Y.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.171, A:Q.171 pi-Stacking: A:Y.197 NCA.16: 7 residues within 4Å: Chain B: A.24, P.33, T.34, F.35, N.101, I.102, D.103 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.27, B:I.102, B:D.103, B:D.103 pi-Stacking: B:F.35

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

2PE.9: 17 residues within 4Å: Chain A: 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.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.197 Water bridges: A:R.43, A:S.67, A:H.118

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

EDO.10: 2 residues within 4Å: Chain A: R.61, Y.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.61 EDO.11: 7 residues within 4Å: Chain A: K.159, R.161, V.162, V.163, E.167, P.168 Chain B: R.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.167

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

PG4.17: 8 residues within 4Å: Chain B: F.35, A.51, F.63, S.67, H.118, V.163, F.165 Ligands: NAD.15 No protein-ligand interaction detected (PLIP)

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

PGE.18: 5 residues within 4Å: Chain B: I.32, K.71, D.72, M.121, W.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.72

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

NAD-dependent deacetylase 2

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