SMTL ID : 4ts3.1

Wild type E. Coli purine nucleoside phosphorylase with 2 FMC molecules in active sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

2 x FMC: (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol(Non-covalent)

FMC.1: 16 residues within 4Å: Chain A: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204 Chain D: H.4, R.43, I.71 Ligands: PO4.2 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.87, A:S.90, A:M.180, A:E.181, A:S.203, A:D.204, A:D.204, D:H.4, D:R.43 FMC.8: 16 residues within 4Å: Chain C: H.4, R.43 Chain F: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204, I.206 Ligands: PO4.7 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:R.87, F:S.90, F:M.180, F:E.181, F:S.203, F:D.204, F:D.204, F:R.217, C:H.4, C:R.43

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

PO4.2: 10 residues within 4Å: Chain A: P.19, G.20, R.24, R.87, V.88, G.89, S.90, E.181 Chain D: R.43 Ligands: FMC.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.20, A:S.90, A:E.181 Salt bridges: A:R.24, A:R.87, D:R.43 PO4.3: 8 residues within 4Å: Chain B: P.19, G.20, R.87, V.88, G.89, S.90, E.181 Chain E: R.43 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:G.20, B:D.21, B:S.90, B:S.90 Water bridges: B:R.24, B:E.181, B:E.181 Salt bridges: B:R.87, E:R.43 PO4.4: 7 residues within 4Å: Chain C: P.19, G.20, R.87, V.88, G.89, S.90 Chain F: R.43 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.20, C:S.90, C:S.90, C:S.90 Water bridges: C:D.21, C:D.21 Salt bridges: C:R.87, F:R.43 PO4.5: 7 residues within 4Å: Chain A: R.43 Chain D: P.19, G.20, R.87, V.88, G.89, S.90 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain D Salt bridges: A:R.43, D:R.87 Hydrogen bonds: D:G.20, D:S.90, D:S.90 Water bridges: D:D.21, D:D.21 PO4.6: 7 residues within 4Å: Chain B: R.43 Chain E: P.19, G.20, R.87, V.88, G.89, S.90 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:G.20, E:V.88, E:S.90, E:S.90 Water bridges: E:D.21, E:D.21 Salt bridges: E:R.87, B:R.43 PO4.7: 10 residues within 4Å: Chain C: R.43 Chain F: P.19, G.20, R.24, R.87, V.88, G.89, S.90, E.181 Ligands: FMC.8 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:G.20, F:D.21, F:V.88, F:S.90, F:S.90 Salt bridges: F:R.24, F:R.87, C:R.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stefanic, Z. et al., Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis. Sci Rep (2018)

Release Date

2015-07-08

Peptides

Purine nucleoside phosphorylase DeoD-type: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Purine nucleoside phosphorylase DeoD-type

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