SMTL ID : 3bm4.1

Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In complex with magnesium and AMPcpr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: A.96, E.116 Ligands: MG.2, ADV.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.96, A:E.116, H2O.1, H2O.4 MG.2: 7 residues within 4Å: Chain A: A.96, E.112, E.116, E.166 Ligands: MG.1, MG.3, ADV.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.112, A:E.116, H2O.6, H2O.6 MG.3: 3 residues within 4Å: Chain A: E.112 Ligands: MG.2, ADV.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.112, H2O.2, H2O.3, H2O.5 MG.4: 4 residues within 4Å: Chain B: A.96, E.116 Ligands: MG.5, ADV.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.96, B:E.116, H2O.8, H2O.8 MG.5: 7 residues within 4Å: Chain B: A.96, E.112, E.116, E.166 Ligands: MG.4, MG.6, ADV.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.112, B:E.116, H2O.8, H2O.13 MG.6: 3 residues within 4Å: Chain B: E.112 Ligands: MG.5, ADV.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.112, H2O.8, H2O.10, H2O.11

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

ADV.7: 20 residues within 4Å: Chain A: W.28, V.29, R.51, R.84, A.96, G.97, L.98, E.112, E.116, M.132, I.141, E.166 Chain B: W.46, E.47, D.133, P.134, G.135 Ligands: MG.1, MG.2, MG.3 28 PLIP interactions: 21 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.51, A:R.84, A:R.84, A:L.98, A:E.166, A:E.166, B:E.47, B:E.47, B:G.135 Water bridges: A:R.51, A:R.51, A:R.51, A:Q.82, A:Q.82, A:Q.82, A:A.96, A:R.111, A:G.165, A:D.194, A:R.196, B:D.133 Salt bridges: A:R.84, A:R.196 pi-Stacking: A:W.28, A:W.28, B:W.46, B:W.46, B:W.46 ADV.8: 20 residues within 4Å: Chain A: W.46, E.47, D.133, P.134, G.135, L.136 Chain B: W.28, V.29, R.51, R.84, A.96, G.97, L.98, E.112, E.116, M.132, E.166 Ligands: MG.4, MG.5, MG.6 24 PLIP interactions: 6 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:E.47, A:E.47, A:G.135, B:R.51, B:R.51, B:R.51, B:R.84, B:R.84, B:L.98, B:E.166, B:E.166 pi-Stacking: A:W.46, A:W.46, A:W.46, B:W.28, B:W.28, B:W.28 Water bridges: B:R.51, B:Q.82, B:A.96, B:R.111, B:D.194 Salt bridges: B:R.84, B:R.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zha, M. et al., Molecular Mechanism of ADP-Ribose Hydrolysis By Human NUDT5 From Structural and Kinetic Studies. J.Mol.Biol. (2008)

Release Date

2008-05-20

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-sugar pyrophosphatase