SMTL ID : 3h95.1

Crystal structure of the NUDIX domain of NUDT6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 11 residues within 4Å: Chain A: A.174, V.175, Y.176, Y.181 Chain B: K.49, L.50, K.55, R.92, T.144, I.146 Ligands: GOL.5 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:V.175, A:Y.176, B:T.147 Water bridges: A:T.177, A:Y.181, B:K.49, B:K.55, B:T.144, B:T.144 Salt bridges: B:K.49, B:K.55, B:K.55 FLC.4: 11 residues within 4Å: Chain A: K.49, L.50, K.55, R.92, T.144, I.146 Chain B: A.174, V.175, Y.176, Y.181 Ligands: GOL.2 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:V.175, B:Y.176, B:Y.181, A:T.144 Water bridges: B:T.177, A:K.49, A:K.55, A:I.146 Salt bridges: A:K.49, A:K.55, A:K.55

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: A.30, K.55, F.56, R.92, Y.107, I.146, T.147 Ligands: FLC.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.56, A:R.92, A:Y.107 Water bridges: A:G.58 GOL.3: 3 residues within 4Å: Chain A: E.36, S.37, Y.158 No protein-ligand interaction detected (PLIP) GOL.5: 8 residues within 4Å: Chain B: A.30, K.55, F.56, R.92, Y.107, I.146, T.147 Ligands: FLC.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.56, B:R.92, B:Y.107, B:Y.107 Water bridges: B:G.58 GOL.6: 3 residues within 4Å: Chain B: E.36, S.37, Y.158 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tresaugues, L. et al., Crystal structure of the NUDIX domain of NUDT6. To be Published

Release Date

2009-07-07

Peptides

Nucleoside diphosphate-linked moiety X motif 6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nucleoside diphosphate-linked moiety X motif 6