SMTL ID : 4eb8.1

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) 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 PO4: PHOSPHATE ION(Non-functional Binders)

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

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)

IM5.2: 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, W.292, V.295 Chain C: F.194 Ligands: PO4.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.68, A:Y.123, A:N.278, A:N.278 Water bridges: A:H.121, A:E.236, A:E.236, A:M.254 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, W.292, V.295 Ligands: PO4.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.68, B:H.121, B:Y.123, B:N.278, B:N.278 Water bridges: B:E.236, B:E.236, B:M.254 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, W.292, V.295 Ligands: PO4.6 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.68, C:N.278, C:N.278 Water bridges: C:E.236 Salt bridges: C:E.236 pi-Stacking: C:F.235

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

EDO.5: 7 residues within 4Å: Chain B: Y.45, Y.129, T.132, F.133, R.136, P.181, V.262 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.132, B:P.181 EDO.8: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suarez, J. et al., Catalytic Site Conformations in Human PNP by (19)F-NMR and Crystallography. Chem.Biol. (2013)

Release Date

2013-02-06

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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