SMTL ID : 3t8i.1

Structural analysis of thermostable S. solfataricus purine-specific nucleoside hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.9, D.14, N.36, I.121, D.238 Ligands: GOL.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.9, A:D.14, A:I.121, A:D.238, H2O.4 CA.8: 6 residues within 4Å: Chain B: D.9, D.14, N.36, I.121, D.238 Ligands: GOL.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.9, B:D.14, B:I.121, B:D.238, H2O.13 CA.17: 6 residues within 4Å: Chain C: D.9, D.14, N.36, I.121, D.238 Ligands: GOL.18 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.9, C:D.14, C:I.121, C:D.238, H2O.25 CA.23: 6 residues within 4Å: Chain D: D.9, D.14, N.36, I.121, D.238 Ligands: GOL.24 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.9, D:D.14, D:I.121, D:D.238, H2O.31

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: N.36, I.121, M.147, N.155, E.161, F.162, N.163, W.186, P.237, D.238 Ligands: CA.1 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: K.143, F.179, D.180, I.181, L.256, N.284, A.285 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: F.151, W.275 Chain D: K.153 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: V.75, V.78, N.155, W.186, L.221, Y.224 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain B: I.121, M.147, N.155, E.161, F.162, N.163, P.237, D.238 Ligands: CA.8 Ligand excluded by PLIP GOL.10: 1 residues within 4Å: Chain B: K.282 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain B: F.151, W.275 Chain C: K.153 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain B: V.138, K.139, V.141, K.142, K.143, G.178, F.179, D.180 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: R.2, H.246, D.247, N.248 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain B: V.78, N.155, W.186, L.221 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain B: W.72, T.74 Ligand excluded by PLIP GOL.18: 10 residues within 4Å: Chain C: I.121, M.147, N.155, E.161, F.162, N.163, P.237, D.238 Ligands: CA.17, GOL.19 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain C: N.36, V.75, V.78, H.79, N.155, F.162, W.186, Y.224 Ligands: GOL.18 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain C: F.151, W.275, L.289 Ligand excluded by PLIP GOL.24: 10 residues within 4Å: Chain D: N.36, I.121, M.147, N.155, E.161, F.162, N.163, P.237, D.238 Ligands: CA.23 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain D: W.72, R.73, T.74 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain D: V.75, V.78, N.155, T.156, F.162, Y.224 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: L.69, N.71 Chain B: K.172, L.263 Chain C: K.266 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:L.69, A:N.71, C:K.266 Water bridges: C:K.266, B:D.176 EDO.7: 4 residues within 4Å: Chain A: N.71, W.72, R.73, W.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.72, A:R.73 EDO.16: 3 residues within 4Å: Chain B: R.198, E.201, Y.202 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.205 EDO.22: 7 residues within 4Å: Chain C: F.179, D.180, I.181, L.256, N.284, A.285, E.286 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.181, C:N.284, C:E.286

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.21: 3 residues within 4Å: Chain C: W.72, R.73, T.74 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.74, C:T.74 PEG.27: 7 residues within 4Å: Chain C: R.66, L.69 Chain D: Y.131, K.172, I.173, D.176, A.177 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.131, D:K.172, D:D.176, C:R.66, C:R.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minici, C. et al., New Determinants in the Catalytic Mechanism of Nucleoside Hydrolases from the Structures of Two Isozymes from Sulfolobus solfataricus. Biochemistry (2012)

Release Date

2012-05-16

Peptides

Purine nucleosidase, (IunH-2): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Purine nucleosidase, (IunH-2)