SMTL ID : 2dsd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: Q.84, R.86, A.98, E.118 Ligands: AMP.4 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.118, A:E.118, H2O.1, AMP.4 MG.2: 5 residues within 4Å: Chain A: E.114, E.117, E.118, E.168 Ligands: AMP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.114, A:E.118, A:E.168, AMP.4 MG.3: 4 residues within 4Å: Chain A: G.99, L.100, E.114 Ligands: AMP.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.114, AMP.4 MG.5: 6 residues within 4Å: Chain B: Q.84, R.86, A.98, E.118, E.168 Ligands: AMP.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.98, B:E.118, H2O.3, H2O.4 MG.6: 6 residues within 4Å: Chain B: E.114, E.117, E.118, E.168 Ligands: MG.7, AMP.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.114, B:E.118, B:E.168 MG.7: 4 residues within 4Å: Chain B: R.113, E.114 Ligands: MG.6, AMP.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.114, AMP.8

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 14 residues within 4Å: Chain A: W.30, R.53, A.98, G.99, L.100, E.114, E.118, E.168 Chain B: T.47, W.48, E.49 Ligands: MG.1, MG.2, MG.3 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.53, A:A.98, A:A.98, A:L.100, A:E.118, A:E.168, A:E.168, B:E.49, B:E.49 pi-Stacking: A:W.30, A:W.30, B:W.48, B:W.48, B:W.48 AMP.8: 15 residues within 4Å: Chain A: T.47, W.48, E.49 Chain B: W.30, V.31, R.53, A.98, G.99, L.100, E.114, E.118, E.168 Ligands: MG.5, MG.6, MG.7 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.53, B:R.53, B:A.98, B:L.100, B:E.114, A:E.49, A:E.49 Water bridges: B:R.86, B:R.86, B:R.86 pi-Stacking: B:W.30, B:W.30, A:W.48, A:W.48, A: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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