SMTL ID : 8d24.1

Crystal structure of Plasmodium falciparum GRP78-NBD in complex with VER155008

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x 3FD: 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile(Non-covalent)

3FD.1: 18 residues within 4Å: Chain A: T.31, Y.32, I.54, P.56, Y.58, K.73, G.217, G.245, E.246, E.283, K.286, R.287, S.290, G.354, S.355, R.357, I.358, D.381 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.32 Hydrogen bonds: A:K.286, A:K.286, A:R.287, A:S.290, A:R.357

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: G.29, T.30, T.31, Y.32, G.216, G.217, G.218, T.219 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.30, A:T.30, A:T.31, A:G.217, A:G.218, A:T.219, A:T.219 Water bridges: A:K.88, A:G.216 SO4.3: 1 residues within 4Å: Chain A: K.263 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.263, A:K.263 Salt bridges: A:K.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mrozek, A. et al., A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues. Front Mol Biosci (2022)

Release Date

2023-05-31

Peptides

Chaperone DnaK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chaperone DnaK

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