SMTL ID : 3hiv.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

1 x TXN: (2R,3R,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-2-({[(S)-({(3R,4R)-4-({[(S)-{[(2R,3R,4R,5R)-5-(2-amino-6-oxo-6,8-dihydro-9H-purin-9-yl)-2-(hydroxymethyl)-4-methoxytetrahydrofuran-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]pyrrolidin-3-yl}oxy)(hydroxy)phosphoryl]oxy}methyl)-4-methoxytetrahydrofuran-3-yl 3-hydroxypropyl hydrogen (S)-phosphate(Non-covalent)

TXN.1: 20 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, 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:N.71, A:Y.73, A:V.74, A:E.121, A:E.121, A:E.121, A:Y.123, A:R.177, A:R.177, A:N.207, A:N.207, A:G.210, A:Y.233 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
B

Vacuolar saporin

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