SMTL ID : 7y4m.1

Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x IWQ: (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-6-(phenylmethoxycarbonylamino)hexanoic acid(Non-covalent)

IWQ.1: 23 residues within 4Å: Chain A: R.55, N.85, A.86, Y.87, V.88, V.89, F.100, H.101, P.102, D.103, D.107, I.111, G.128, N.129, Y.130, I.179, S.183, E.184, R.187, N.216, W.218, G.219, R.265 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:N.85, A:Y.87, A:Y.87, A:V.89, A:F.100, A:P.102, A:D.107, A:I.111 Hydrogen bonds: A:R.55, A:N.85, A:V.88, A:V.88, A:V.88, A:Y.130, A:S.183, A:R.187, A:R.187 Water bridges: A:Y.87, A:N.129, A:D.131, A:E.215 pi-Stacking: A:Y.87, A:Y.130, A:W.218 pi-Cation interactions: A:Y.87

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

SO4.2: 2 residues within 4Å: Chain A: T.24, Q.26 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.24, A:Q.26 SO4.3: 3 residues within 4Å: Chain A: F.126, G.127, R.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.127 Salt bridges: A:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saito, R. et al., Pterin-based small molecule inhibitor capable of binding to the secondary pocket in the active site of ricin-toxin A chain. Plos One (2022)

Release Date

2022-11-16

Peptides

Ricin A chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ricin A chain

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