SMTL ID : 1yc2.10 (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: 3 residues within 4Å: Chain A: H.17, E.180, H.183 3 PLIP interactions: 3 interactions with chain A Metal complexes: 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: 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

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

SO4.3: 4 residues within 4Å: Chain A: P.170, Q.171, R.172, T.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.172, A:T.173, A:T.173 SO4.4: 3 residues within 4Å: Chain A: K.123, T.132, R.161 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.123, A:R.161 SO4.5: 1 residues within 4Å: Chain A: K.182 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.182 SO4.10: 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.6: 26 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, N.217, A.218, E.219, G.233, K.234, A.235 Ligands: 2PE.7 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.24, A:F.35 Hydrogen bonds: A:A.24, A:G.25, A:S.27, A:E.29, A:F.35, A:R.36, A:R.36, A:Q.100, A:Q.100, A:N.101, A:I.102, A:D.103, A:D.103, A:S.192, A:S.193, A:S.193, A:N.217, A:A.218, A:E.219, A:A.235 NAD.11: 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: PG4.13 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

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

2PE.7: 10 residues within 4Å: Chain A: I.32, F.66, S.67, I.102, H.118, V.163, F.165, L.169, Y.197 Ligands: NAD.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.169

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.12: 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 PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.13: 9 residues within 4Å: Chain A: M.222 Chain B: F.35, A.51, F.63, S.67, H.118, V.163, F.165 Ligands: NAD.11 No protein-ligand interaction detected (PLIP)

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

PGE.14: 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
C

B
D

NAD-dependent deacetylase 2

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