SMTL ID : 1szd.2 (1 other biounit)

Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: K.29, W.205, K.209 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: K.29, W.205, K.209 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.146, C.149, C.173, C.176 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.146, A:C.149, A:C.173, A:C.176 ZN.8: 4 residues within 4Å: Chain C: C.146, C.149, C.173, C.176 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.146, C:C.149, C:C.173, C:C.176

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

APR.3: 21 residues within 4Å: Chain A: G.35, A.36, G.37, T.40, F.47, R.48, E.67, Q.118, F.187, G.226, T.227, S.228, V.231, N.251, L.252, Q.271, Y.272, S.273 Chain B: K.5, H.7 Chain C: P.50 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.36, A:G.37, A:T.40, A:T.40, A:E.67, A:Q.118, A:T.227, A:S.228, A:S.228, A:N.251, A:L.252, A:S.273, B:H.7 Water bridges: A:T.40, A:R.48, A:R.48, A:R.48, A:R.48, A:R.48, A:R.48, A:R.48, A:R.48, A:S.228 Salt bridges: A:R.48, A:R.48 APR.9: 21 residues within 4Å: Chain A: P.50 Chain C: G.35, A.36, G.37, T.40, F.47, R.48, E.67, Q.118, F.187, G.226, T.227, S.228, V.231, N.251, L.252, Q.271, Y.272, S.273 Chain D: K.5, H.7 23 PLIP interactions: 22 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.36, C:G.37, C:T.40, C:Q.118, C:S.228, C:S.228, C:N.251, C:L.252, C:S.273, D:H.7 Water bridges: C:T.40, C:R.48, C:R.48, C:R.48, C:R.48, C:R.48, C:R.48, C:R.48, C:R.48, C:S.228, C:E.253 Salt bridges: C:R.48, C:R.48

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: S.196, W.199, S.236, E.240 Chain B: K.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.196, A:W.199 Water bridges: A:S.203, A:S.236, B:G.2 GOL.5: 3 residues within 4Å: Chain A: P.45, T.52, G.53 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.53, A:G.53, A:L.54, A:E.88 GOL.6: 6 residues within 4Å: Chain A: K.87, Y.90, N.93, K.159, L.162, A.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.87, A:N.93, A:L.162 GOL.10: 5 residues within 4Å: Chain C: S.196, W.199, S.236, E.240 Chain D: K.1 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.196, C:W.199 Water bridges: C:S.203, C:S.236, C:E.240, D:G.2 GOL.11: 3 residues within 4Å: Chain C: P.45, T.52, G.53 4 PLIP interactions: 4 interactions with chain C Water bridges: C:G.53, C:G.53, C:L.54, C:E.88 GOL.12: 6 residues within 4Å: Chain C: K.87, Y.90, N.93, K.159, L.162, A.163 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.87, C:N.93, C:L.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, K. et al., Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases. Proc.Natl.Acad.Sci.Usa (2004)

Release Date

2004-06-15

Peptides

NAD-dependent deacetylase HST2: AC
Histone H4 peptide: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

NAD-dependent deacetylase HST2

Histone H4 peptide

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