SMTL ID : 1szc.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 1.75 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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 CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: R.207, R.243 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain C: R.207, R.243 Ligand excluded by PLIP

2 x CNA: CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

CNA.3: 27 residues within 4Å: Chain A: G.35, A.36, G.37, S.39, T.40, I.44, D.46, F.47, R.48, Q.118, N.119, I.120, D.121, F.187, G.226, T.227, S.228, L.229, V.231, N.251, L.252, E.253, Q.271, Y.272, S.273 Chain B: K.5 Chain C: P.50 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.36 Hydrogen bonds: A:A.36, A:T.40, A:T.40, A:I.120, A:D.121, A:D.121, A:G.226, A:T.227, A:S.228, A:S.228, A:L.229, A:N.251, A:L.252, A:E.253, A:S.273 Water bridges: A:T.40, A:D.46, A:R.48, A:R.48, A:E.253 Salt bridges: A:R.48 CNA.10: 27 residues within 4Å: Chain A: P.50 Chain C: G.35, A.36, G.37, S.39, T.40, I.44, D.46, F.47, R.48, Q.118, N.119, I.120, D.121, F.187, G.226, T.227, S.228, L.229, V.231, N.251, L.252, E.253, Q.271, Y.272, S.273 Chain D: K.5 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:A.36 Hydrogen bonds: C:A.36, C:T.40, C:I.120, C:D.121, C:D.121, C:D.121, C:G.226, C:S.228, C:S.228, C:L.229, C:N.251, C:L.252, C:E.253, C:S.273 Water bridges: C:T.40, C:R.48, C:R.48, C:E.253 Salt bridges: C:R.48

8 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.196, A:W.199 GOL.5: 2 residues within 4Å: Chain A: T.52, G.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.52 Water bridges: A:G.53, A:G.53, A:E.88, A:E.88 GOL.6: 5 residues within 4Å: Chain A: K.87, Y.90, N.93, L.162, A.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.87, A:N.93, A:L.162 GOL.7: 4 residues within 4Å: Chain A: K.29, K.113, W.205, K.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.113, A:K.113, A:K.209, A:K.209 GOL.11: 5 residues within 4Å: Chain C: S.196, W.199, S.236, E.240 Chain D: K.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.196, C:W.199 GOL.12: 2 residues within 4Å: Chain C: T.52, G.53 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.52, C:T.52 Water bridges: C:G.53, C:G.53, C:E.88, C:E.88 GOL.13: 5 residues within 4Å: Chain C: K.87, Y.90, N.93, L.162, A.163 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.87, C:N.93, C:L.162 GOL.14: 4 residues within 4Å: Chain C: K.29, K.113, W.205, K.209 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.113, C:K.113, C:K.209, C:K.209

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

Related Entries With Identical Sequence