SMTL ID : 5ugf.1 (1 other biounit)

Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

16 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: G.63, S.64, H.95, R.115, H.117, N.146, A.147, S.251 Ligands: IM5.8 Ligand excluded by PLIP PO4.2: 4 residues within 4Å: Chain A: R.179 Chain C: Y.122, P.123, Q.175 Ligand excluded by PLIP PO4.3: 4 residues within 4Å: Chain A: N.182, D.183, E.184, R.185 Ligand excluded by PLIP PO4.4: 3 residues within 4Å: Chain A: R.164 Chain C: R.238, Y.280 Ligand excluded by PLIP PO4.5: 3 residues within 4Å: Chain A: R.238, Y.280 Chain B: R.164 Ligand excluded by PLIP PO4.6: 5 residues within 4Å: Chain A: R.164, R.199, R.202, E.220 Chain C: Y.280 Ligand excluded by PLIP PO4.7: 2 residues within 4Å: Chain A: D.195, R.260 Ligand excluded by PLIP PO4.9: 9 residues within 4Å: Chain B: G.63, S.64, H.95, R.115, H.117, N.146, A.147, S.251 Ligands: IM5.14 Ligand excluded by PLIP PO4.10: 5 residues within 4Å: Chain A: Y.122, P.123, Q.175 Chain B: M.32, R.179 Ligand excluded by PLIP PO4.11: 3 residues within 4Å: Chain B: R.238, Y.280 Chain C: R.164 Ligand excluded by PLIP PO4.12: 2 residues within 4Å: Chain B: T.74, Q.75 Ligand excluded by PLIP PO4.13: 4 residues within 4Å: Chain B: T.37, Y.38, E.39, R.185 Ligand excluded by PLIP PO4.15: 9 residues within 4Å: Chain C: G.63, S.64, H.95, R.115, H.117, N.146, A.147, S.251 Ligands: IM5.19 Ligand excluded by PLIP PO4.16: 3 residues within 4Å: Chain B: P.123, Q.175 Chain C: R.179 Ligand excluded by PLIP PO4.17: 5 residues within 4Å: Chain B: Y.280 Chain C: R.164, R.199, R.202, Q.203 Ligand excluded by PLIP PO4.18: 4 residues within 4Å: Chain C: T.37, Y.38, E.39, R.185 Ligand excluded by PLIP

3 x IM5: 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

IM5.8: 19 residues within 4Å: Chain A: S.64, H.117, Y.119, A.147, A.148, G.149, V.226, F.231, E.232, V.248, G.249, M.250, T.273, N.274, V.276, H.288, V.291 Chain B: Y.190 Ligands: PO4.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.64, A:N.274, A:N.274, A:H.288 Water bridges: A:H.117, A:E.232, A:M.250 Salt bridges: A:E.232 pi-Stacking: A:F.231 Hydrophobic interactions: B:Y.190 IM5.14: 19 residues within 4Å: Chain B: S.64, H.117, Y.119, A.147, A.148, G.149, V.226, F.231, E.232, V.248, G.249, M.250, T.273, N.274, V.276, H.288, V.291 Chain C: Y.190 Ligands: PO4.9 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.64, B:Y.119, B:N.274, B:N.274, C:Y.190 Water bridges: B:H.117, B:E.232, B:E.232, B:M.250 Salt bridges: B:E.232 pi-Stacking: B:F.231 Hydrophobic interactions: C:Y.190 IM5.19: 19 residues within 4Å: Chain A: Y.190 Chain C: S.64, H.117, Y.119, A.147, A.148, G.149, V.226, F.231, E.232, V.248, G.249, M.250, T.273, N.274, V.276, H.288, V.291 Ligands: PO4.15 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:Y.190 Water bridges: A:Y.190, C:H.117, C:E.232, C:M.250 Hydrogen bonds: C:T.273, C:N.274, C:N.274, C:H.288 Salt bridges: C:E.232 pi-Stacking: C:F.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harijan, R.K. et al., Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-06-21

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Purine nucleoside phosphorylase

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