SMTL ID : 5a3c.1

Crystal structure of the ADP-ribosylating sirtuin (SirTM) from Streptococcus pyogenes in complex with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

3 x GLY: GLYCINE(Non-covalent)

GLY.1: 5 residues within 4Å: Chain A: Y.70, Q.71, F.72, Q.77, F.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.70, A:Q.77 GLY.2: 3 residues within 4Å: Chain A: D.85, W.86, Q.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.86, A:Q.87 GLY.3: 5 residues within 4Å: Chain A: K.120, D.121, Y.122, N.142, F.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.122, A:Y.122, A:N.142

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.155, C.159, C.190, C.193 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.155, A:C.159, A:C.190, A:C.193

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

NAD.5: 24 residues within 4Å: Chain A: G.43, A.44, G.45, A.49, Y.54, L.76, T.127, N.128, A.129, D.130, Q.147, Y.150, G.239, V.240, G.241, H.242, T.243, T.244, N.268, H.269, K.270, Y.272, H.288, I.289 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.44, A:Y.54, A:Y.54 Hydrogen bonds: A:A.44, A:T.127, A:T.127, A:A.129, A:D.130, A:D.130, A:Q.147, A:Y.150, A:V.240, A:G.241, A:H.242, A:T.243, A:T.243, A:T.244, A:T.244, A:N.268, A:H.269, A:H.288, A:I.289 Water bridges: A:Q.104, A:T.244, A:Y.272 pi-Stacking: A:H.269, A:H.269

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

EDO.6: 5 residues within 4Å: Chain A: Y.89, Q.154, E.198, I.199, K.201 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.154, A:E.198, A:K.201 Water bridges: A:S.79, A:L.80 EDO.7: 6 residues within 4Å: Chain A: F.81, D.82, F.83, D.85, W.86, Y.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.81, A:F.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rack, J.G. et al., Identification of a Class of Protein Adp-Ribosylating Sirtuins in Microbial Pathogens. Mol.Cell (2015)

Release Date

2015-07-29

Peptides

SIR2 FAMILY PROTEIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SIR2 FAMILY PROTEIN

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