SMTL ID : 3ggs.1

Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoro-2'-deoxyadenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-trimer

Ligands

4 x 2FD: 5-(6-AMINO-2-FLUORO-PURIN-9-YL)-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-OL(Non-covalent)

2FD.1: 16 residues within 4Å: Chain A: S.55, Y.110, A.138, A.139, G.140, V.217, F.222, Q.223, V.239, G.240, M.241, T.264, D.265, V.267 Chain C: F.181 Ligands: SO4.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.138 Hydrogen bonds: A:Y.110, A:Y.110, A:A.138, A:Q.223 Water bridges: A:M.241, A:M.241, A:S.242 pi-Stacking: A:F.222, A:F.222 2FD.12: 14 residues within 4Å: Chain A: F.181 Chain B: A.138, G.140, V.217, F.222, Q.223, V.239, G.240, M.241, T.264, D.265, V.267, V.282 Ligands: SO4.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.138, B:Q.223 Water bridges: B:Q.223, B:M.241 pi-Stacking: B:F.222, B:F.222 2FD.23: 15 residues within 4Å: Chain B: F.181 Chain C: S.55, Y.110, A.138, A.139, G.140, F.222, Q.223, V.239, G.240, M.241, T.264, D.265, V.267 Ligands: SO4.24 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.55, C:Y.110, C:Y.110, C:Q.223, C:T.264, C:D.265 Water bridges: C:Q.223 pi-Stacking: C:F.222 2FD.34: 4 residues within 4Å: Chain C: K.44, Q.66, F.94, G.97 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.94 Hydrogen bonds: C:K.44, C:Q.66 pi-Stacking: C:F.94

30 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: G.54, S.55, R.106, H.108, N.137, A.138, S.242 Ligands: 2FD.1 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: P.114, Q.166 Chain C: R.170 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: R.170 Chain B: M.23, P.114, Q.166 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: S.55, G.56, L.57, G.58, Q.104 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: F.78, P.79, R.80, K.117 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain A: R.251 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: R.155, R.190, R.193 Chain B: Y.271, E.275 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: N.143, K.145 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: G.286, K.287, Q.288, A.289 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: T.28, Y.29, E.30, R.176 Ligand excluded by PLIP SO4.13: 8 residues within 4Å: Chain B: G.54, S.55, R.106, H.108, N.137, A.138, S.242 Ligands: 2FD.12 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: R.251, G.254 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain B: G.54, S.55, G.56, L.57, G.58, H.86, Q.104 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: T.28, Y.29, E.30, R.176 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: R.155, R.190, R.193 Chain C: Y.271 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain B: R.46 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: D.62, I.69, R.89 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: R.195, P.305 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: G.286, K.287, Q.288, A.289 Ligand excluded by PLIP SO4.22: 1 residues within 4Å: Chain B: N.143 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain C: G.54, S.55, R.106, H.108, N.137, A.138, S.242 Ligands: 2FD.23 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: R.170 Chain C: P.114, Q.166 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain C: G.54, S.55, G.56, L.57, G.58, Q.104 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: R.195, P.305, L.306 Ligand excluded by PLIP SO4.28: 1 residues within 4Å: Chain C: R.251 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain C: N.143, K.145 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain C: F.78, P.79, R.80, K.117 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain A: E.275 Chain C: R.155, R.190, R.193 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain B: R.155 Chain C: R.229, Y.271 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain C: S.198, K.201 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Afshar, S. et al., Structure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine. Protein Sci. (2009)

Release Date

2009-04-14

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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