SMTL ID : 3hit.1 (1 other biounit)

Crystal structure of Saporin-L1 in complex with the dinucleotide inhibitor, a transition state analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

monomer

Ligands

1 x DYN: 5'-O-[(S)-{[(3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[(S)-hydroxy(3-hydroxypropoxy)phosphoryl]oxy}methyl)pyrrolidin-3-yl]oxy}(hydroxy)phosphoryl]-3'-O-[(R)-hydroxy(4-hydroxybutoxy)phosphoryl]-2'-O-methylguanosine(Non-covalent)

DYN.1: 21 residues within 4Å: Chain A: N.71, L.72, Y.73, V.74, F.91, F.94, E.121, S.122, Y.123, P.124, V.169, E.174, R.177, E.206, N.207, N.208, W.209, G.210, R.214, Y.233, L.254 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.123 Hydrogen bonds: A:Y.73, A:V.74, A:E.121, A:E.121, A:Y.123, A:R.177, A:R.177, A:N.207, A:N.207, A:W.209, A:G.210, A:Y.233 Water bridges: A:N.71 Salt bridges: A:E.121, A:E.174, A:R.214 pi-Stacking: A:Y.73, A:Y.73, A:Y.73 pi-Cation interactions: A:Y.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ho, M.C. et al., Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-12-08

Peptides

Vacuolar saporin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vacuolar saporin

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