SMTL ID : 1su2.1

CRYSTAL STRUCTURE OF THE NUDIX HYDROLASE DR1025 IN COMPLEX WITH ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: L.13, R.14, A.51 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.2: 6 residues within 4Å: Chain A: A.15, S.49, G.50, R.95 Chain B: M.1 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.49 MG.3: 1 residues within 4Å: Chain A: E.65 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.65, H2O.2, H2O.3, H2O.3, H2O.4 MG.5: 6 residues within 4Å: Chain A: M.1 Chain B: A.15, S.49, G.50, R.95 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.49 MG.6: 4 residues within 4Å: Chain B: L.13, R.14, A.51 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: R.64, E.65 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.65, H2O.7, H2O.8, H2O.9, H2O.12

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 16 residues within 4Å: Chain A: L.13, A.15, S.49, G.50, A.51, F.87, D.89, V.91, I.93, R.95 Chain B: M.1, E.2, D.4, R.6 Ligands: MG.1, MG.2 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.89, A:R.95, B:M.1, B:D.4, B:R.6 Water bridges: A:A.51, A:A.51, A:D.89 pi-Stacking: A:F.87, A:F.87 Salt bridges: B:R.6 ATP.8: 15 residues within 4Å: Chain A: M.1, E.2, D.4, R.6 Chain B: L.13, A.15, G.50, A.51, F.87, D.89, V.91, I.93, R.95 Ligands: MG.5, MG.6 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:M.1, A:M.1, A:E.2, A:E.2, A:E.2, A:D.4, A:D.4, B:D.89, B:V.91 Salt bridges: A:R.6, B:R.95 Water bridges: B:D.89, B:D.89 pi-Stacking: B:F.87, B:F.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ranatunga, W. et al., Structural Studies of the Nudix Hydrolase DR1025 From Deinococcus radiodurans and its Ligand Complexes. J.Mol.Biol. (2004)

Release Date

2004-05-11

Peptides

MutT/nudix family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MutT/nudix family protein

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