SMTL ID : 5etj.2 (1 other biounit)

Crystal structure of purine nucleoside phosphorylase (E258D, L261A) mutant from human complexed with DADMe-ImmG and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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)

IM5.1: 19 residues within 4Å: Chain A: S.68, H.121, Y.123, A.151, A.152, G.153, V.230, F.235, E.236, V.252, G.253, M.254, T.277, N.278, V.280, H.292, V.295 Chain C: F.194 Ligands: PO4.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.68, A:T.277, A:N.278, A:N.278, A:H.292 Water bridges: A:E.236 Salt bridges: A:E.236 pi-Stacking: A:F.235 IM5.4: 19 residues within 4Å: Chain A: F.194 Chain B: S.68, H.121, Y.123, A.151, A.152, G.153, V.230, F.235, E.236, V.252, G.253, M.254, T.277, N.278, V.280, H.292, V.295 Ligands: PO4.5 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.194 Hydrogen bonds: B:S.68, B:Y.123, B:N.278, B:N.278 Water bridges: B:E.236, B:E.236 Salt bridges: B:E.236 pi-Stacking: B:F.235 IM5.7: 19 residues within 4Å: Chain B: F.194 Chain C: S.68, H.121, Y.123, A.151, A.152, G.153, V.230, F.235, E.236, V.252, G.253, M.254, T.277, N.278, V.280, H.292, V.295 Ligands: PO4.8 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.68, C:H.121, C:Y.123, C:N.278, C:N.278 Water bridges: C:E.236 Salt bridges: C:E.236 pi-Stacking: C:F.235 Hydrophobic interactions: B:F.194

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

PO4.2: 9 residues within 4Å: Chain A: G.67, S.68, H.99, R.119, H.121, N.150, A.151, S.255 Ligands: IM5.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.68, A:S.68, A:S.68, A:A.151, A:A.151, A:S.255 Water bridges: A:M.254 Salt bridges: A:H.99, A:R.119, A:H.121 PO4.3: 4 residues within 4Å: Chain A: M.36, R.183 Chain B: P.127, Q.179 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.183 Hydrogen bonds: B:Q.179, B:Q.179 PO4.5: 9 residues within 4Å: Chain B: G.67, S.68, H.99, R.119, H.121, N.150, A.151, S.255 Ligands: IM5.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.68, B:A.151, B:A.151, B:S.255 Water bridges: B:S.255 Salt bridges: B:H.99, B:R.119, B:H.121 PO4.6: 5 residues within 4Å: Chain B: M.36, R.183 Chain C: M.36, P.127, Q.179 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.183 Hydrogen bonds: C:Q.179 PO4.8: 9 residues within 4Å: Chain C: G.67, S.68, H.99, R.119, H.121, N.150, A.151, S.255 Ligands: IM5.7 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.68, C:A.151, C:S.255, C:S.255, C:S.255 Water bridges: C:M.254 Salt bridges: C:H.99, C:R.119, C:H.121 PO4.9: 5 residues within 4Å: Chain A: M.36, P.127, Q.179 Chain C: M.36, R.183 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Salt bridges: C:R.183 Hydrogen bonds: A:Q.179, A:Q.179 Water bridges: A:L.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zoi, I. et al., Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics. J.Am.Chem.Soc. (2016)

Release Date

2016-09-14

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Purine nucleoside phosphorylase

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