SMTL ID : 8db7.1

Adenosine/guanosine nucleoside hydrolase bound to a fragment inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: D.12, L.125, M.151, N.160, E.166, F.167, N.168, A.238, D.239 Ligands: R2O.2, CA.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.160, A:N.160, A:F.167, A:N.168, A:D.239 Water bridges: A:D.12, A:N.37, A:N.37, A:N.168 GOL.4: 10 residues within 4Å: Chain B: D.12, D.13, N.37, H.80, L.125, M.151, F.167, N.168, D.239 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.37, B:N.168 Water bridges: B:H.80 GOL.6: 12 residues within 4Å: Chain C: D.8, D.12, D.13, N.37, H.80, L.125, M.151, F.167, N.168, D.239 Ligands: R2O.7, CA.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.37, C:N.168 GOL.9: 12 residues within 4Å: Chain D: N.37, H.80, L.125, M.151, N.160, E.166, F.167, N.168, A.238, D.239 Ligands: R2O.10, CA.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.37, D:L.125, D:N.160, D:E.166, D:N.168 Water bridges: D:N.37

3 x R2O: N-(4-fluorophenyl)-4,5-dihydro-1H-imidazol-2-amine(Non-covalent)

R2O.2: 10 residues within 4Å: Chain A: D.12, I.79, N.160, I.161, W.193, I.227, F.230, D.231, C.236 Ligands: GOL.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.79, A:N.160, A:F.230 Hydrogen bonds: A:D.231 pi-Stacking: A:H.80 R2O.7: 10 residues within 4Å: Chain B: P.77, H.78 Chain C: D.12, I.79, G.165, W.193, I.227, D.231, C.236 Ligands: GOL.6 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.79, C:I.79, C:W.193 Hydrogen bonds: C:D.231, C:D.231 pi-Stacking: B:H.78 R2O.10: 10 residues within 4Å: Chain D: D.12, I.79, N.160, I.161, W.193, I.227, F.230, D.231, C.236 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.79, D:I.79, D:N.160 Hydrogen bonds: D:D.231 pi-Stacking: D:F.230

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.8, D.13, N.37, L.125, D.239 Ligands: GOL.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:D.13, A:L.125, A:D.239, H2O.1 CA.5: 6 residues within 4Å: Chain B: D.8, D.13, N.37, L.125, D.239 Ligands: GOL.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, B:D.13, B:D.13, B:L.125, H2O.3 CA.8: 6 residues within 4Å: Chain C: D.8, D.13, N.37, L.125, D.239 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.8, C:D.13, C:D.13, C:L.125, C:D.239 CA.11: 5 residues within 4Å: Chain D: D.8, D.13, L.125, D.239 Ligands: GOL.9 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.13, D:L.125, D:D.239, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muellers, S.N. et al., Structure-Guided Insight into the Specificity and Mechanism of a Parasitic Nucleoside Hydrolase. Biochemistry (2022)

Release Date

2022-09-07

Peptides

Inosine-uridine preferring nucleoside hydrolase family protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

Inosine-uridine preferring nucleoside hydrolase family protein

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