SMTL ID : 1v8v.1

Crystal structure analysis of the ADP-ribose pyrophosphatase of E86Q mutant, complexed with ADP-ribose and Mg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: L.68, R.81, E.82 Ligands: APR.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.82 MG.3: 4 residues within 4Å: Chain B: L.68, R.81, E.82 Ligands: APR.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.82

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

APR.2: 19 residues within 4Å: Chain A: R.18, I.19, H.33, Q.52, R.54, E.63, A.66, G.67, L.68, E.82, E.108 Chain B: R.27, Y.28, E.29, S.102, P.103, G.104, F.105 Ligands: MG.1 20 PLIP interactions: 7 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:E.29, B:E.29, B:E.29, B:S.102, B:G.104, A:R.18, A:R.18, A:Q.52, A:E.63, A:L.68, A:E.108 pi-Stacking: B:Y.28, B:Y.28 Water bridges: A:E.63, A:E.63, A:R.81, A:Q.86, A:Q.86 Salt bridges: A:R.54, A:R.54 APR.4: 19 residues within 4Å: Chain A: R.27, Y.28, E.29, S.102, P.103, G.104, F.105 Chain B: R.18, I.19, H.33, Q.52, R.54, E.63, A.66, G.67, L.68, E.82, E.108 Ligands: MG.3 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.18, B:R.18, B:Q.52, B:E.63, B:L.68, B:E.108, A:E.29, A:E.29, A:S.102, A:G.104 Water bridges: B:R.81, B:Q.86, B:Q.86 Salt bridges: B:R.54, B:R.54 pi-Stacking: A:Y.28, A:Y.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshiba, S. et al., Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal. J.Biol.Chem. (2004)

Release Date

2004-10-19

Peptides

ADP-ribose pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ADP-ribose pyrophosphatase

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