SMTL ID : 1khz.1

Structure of the ADPR-ase in complex with AMPCPR and Mg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 1 residues within 4Å: Chain A: D.5 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain B: A.96, E.112, E.116, E.162, E.164 Ligands: MG.3, MG.4, ADV.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.112, B:E.116, B:E.164, H2O.5, H2O.5 MG.3: 4 residues within 4Å: Chain B: E.112, E.162 Ligands: MG.2, ADV.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.112, H2O.5, H2O.5, H2O.5, H2O.5 MG.4: 6 residues within 4Å: Chain B: R.79, A.96, E.116, E.164 Ligands: MG.2, ADV.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.96, B:E.116, H2O.5, H2O.5

1 x ADV: ALPHA-BETA METHYLENE ADP-RIBOSE(Non-covalent)

ADV.5: 24 residues within 4Å: Chain A: R.51, E.52, I.53, S.133, P.134, G.135, G.136 Chain B: F.28, F.29, R.56, A.59, R.79, E.93, A.96, G.97, M.98, E.112, E.116, E.139, E.162, E.164 Ligands: MG.2, MG.3, MG.4 29 PLIP interactions: 10 interactions with chain A, 19 interactions with chain B Hydrogen bonds: A:R.51, A:E.52, A:S.133, A:G.135, A:G.135, A:G.136, B:R.56, B:R.79, B:R.79, B:E.93, B:M.98, B:E.139, B:E.162, B:E.162, B:E.162 Water bridges: A:R.51, A:R.51, B:R.56, B:R.56, B:Q.77, B:Q.77, B:Q.77, B:Q.77, B:E.93, B:R.111, B:S.141 pi-Cation interactions: A:R.51, A:R.51 Salt bridges: B:R.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabelli, S.B. et al., Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase. Biochemistry (2002)

Release Date

2002-10-09

Peptides

ADP-ribose pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-ribose pyrophosphatase

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