SMTL ID : 5t3p.1

Crystal structure of Human Peroxisomal coenzyme A diphosphatase NUDT7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-trimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Q.95, E.96, G.99, Q.136, N.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.99, A:Q.136 EDO.2: 5 residues within 4Å: Chain A: D.28, V.107, V.108, C.109, C.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.107, A:C.110 EDO.3: 7 residues within 4Å: Chain A: Y.41, R.61, L.65, R.66, R.67 Chain B: K.64 Ligands: EDO.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.41, A:R.61, A:R.66, A:R.67, B:K.64 Water bridges: A:K.78 EDO.4: 4 residues within 4Å: Chain A: Y.41, R.66, K.78 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.41, A:R.66, A:K.78 EDO.5: 6 residues within 4Å: Chain B: D.28, V.107, V.108, C.109, C.110 Chain C: M.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.110 Water bridges: B:G.31 EDO.6: 6 residues within 4Å: Chain A: K.64 Chain B: Y.41, R.66, R.67, K.78 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.41, B:R.66, B:R.66, B:R.67 Water bridges: B:R.67 EDO.7: 5 residues within 4Å: Chain B: N.39, Y.41, R.66, K.78 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.39, B:Y.41, B:R.66, B:K.78, B:K.78 EDO.8: 4 residues within 4Å: Chain C: V.72, T.186, Y.187, Q.188 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.188 EDO.9: 6 residues within 4Å: Chain C: N.39, Y.41, R.66, R.67, K.78 Ligands: EDO.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.41, C:R.66, C:R.66, C:R.67, C:K.78 EDO.10: 5 residues within 4Å: Chain C: Y.41, R.66, R.67, K.78 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.66, C:R.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srikannathasan, V., Crystal structure of Human Peroxisomal coenzyme A diphosphatase NUDT7. To Be Published

Release Date

2017-09-13

Peptides

Peroxisomal coenzyme A diphosphatase NUDT7: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Peroxisomal coenzyme A diphosphatase NUDT7