SMTL ID : 8d1p.1

Crystal structure of Plasmodium falciparum GRP78-NBD in complex with 7-Deaza-2'-C-methyladenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

2 x H5V: 7-(2-C-methyl-beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine(Non-covalent)

H5V.1: 12 residues within 4Å: Chain A: G.216, G.217, G.245, E.246, E.283, K.286, R.287, S.290, G.354, S.355, R.357, I.358 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.287 Hydrogen bonds: A:K.286, A:K.286, A:K.286, A:R.287, A:S.290, A:G.354 Water bridges: A:R.357 H5V.2: 3 residues within 4Å: Chain A: K.262, K.263 Ligands: SO4.4 No protein-ligand interaction detected (PLIP)

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

SO4.3: 7 residues within 4Å: Chain A: G.29, T.30, T.31, G.216, G.217, G.218, T.219 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.30, A:T.30, A:T.31, A:Y.32, A:G.217, A:G.218, A:T.219, A:T.219 Water bridges: A:K.88, A:G.216, A:T.219 SO4.4: 2 residues within 4Å: Chain A: K.263 Ligands: H5V.2 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.263, A:K.263, A:K.263, A:E.310 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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