SMTL ID : 2dsc.1

Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: A.98, E.114, E.118, E.168 Ligands: APR.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.98, A:E.118, H2O.1, H2O.2 MG.3: 4 residues within 4Å: Chain B: A.98, E.114, E.118 Ligands: APR.2 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.98, B:E.118, H2O.6, H2O.7

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

APR.2: 17 residues within 4Å: Chain A: W.48, E.49, D.135, P.136, G.137, L.138 Chain B: W.30, V.31, R.53, R.86, A.98, G.99, L.100, E.114, M.134, E.168 Ligands: MG.3 25 PLIP interactions: 19 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.53, B:R.53, B:L.100, A:E.49, A:E.49, A:D.135, A:G.137 Water bridges: B:Q.84, B:R.86, B:R.86, B:R.86, B:A.98, B:E.168, B:E.168, B:R.198, B:R.198, B:R.198, B:R.198 Salt bridges: B:R.86, B:R.86, B:R.198 pi-Stacking: B:W.30, B:W.30, A:W.48, A:W.48 APR.4: 20 residues within 4Å: Chain A: W.30, V.31, R.53, R.86, E.95, A.98, G.99, L.100, E.114, E.118, M.134, E.168, R.198 Chain B: W.48, E.49, D.135, P.136, G.137, L.138 Ligands: MG.1 28 PLIP interactions: 21 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.53, A:R.53, A:E.95, A:L.100, A:E.118, A:E.168, B:E.49, B:E.49, B:D.135, B:G.137 Water bridges: A:Q.84, A:Q.84, A:Q.84, A:R.86, A:R.86, A:A.98, A:E.114, A:E.114, A:D.166, A:R.198, A:R.198 Salt bridges: A:R.86, A:R.86, A:R.198 pi-Stacking: A:W.30, B:W.48, B:W.48, B:W.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zha, M. et al., Crystal Structures of Human NUDT5 Reveal Insights into the Structural Basis of the Substrate Specificity. J.Mol.Biol. (2006)

Release Date

2006-11-14

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-sugar pyrophosphatase

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