SMTL ID : 7y07.1

Crystal structure of Ricin A chain bound with (S)-2-amino-N-(1-hydroxy-3-phenylpropan-2-yl)-4-oxo-3,4-dihydropteridine-7-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

2 x IFX: 2-azanyl-4-oxidanylidene-N-[(2S)-1-oxidanyl-3-phenyl-propan-2-yl]-3H-pteridine-7-carboxamide(Non-covalent)

IFX.1: 14 residues within 4Å: Chain A: A.86, Y.87, V.88, F.100, G.128, N.129, Y.130, I.179, S.183, E.184, R.187, E.215, N.216 Ligands: IFX.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.216 Hydrogen bonds: A:V.88, A:V.88, A:V.88, A:Y.130, A:S.183, A:R.187, A:R.187 Water bridges: A:D.131 pi-Stacking: A:Y.87, A:Y.130 pi-Cation interactions: A:Y.87 IFX.2: 13 residues within 4Å: Chain A: D.82, N.85, Y.87, V.89, H.101, P.102, D.103, D.107, N.129, R.187, W.218, R.265 Ligands: IFX.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.85 Hydrogen bonds: A:N.85, A:D.103, A:N.129 Water bridges: A:D.82, A:D.107, A:D.107 Salt bridges: A:D.82, A:D.103, A:D.107 pi-Stacking: A:Y.87, A:Y.87, A:W.218

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

SO4.3: 2 residues within 4Å: Chain A: T.24, Q.26 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.24, A:V.25 SO4.4: 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

Goto, M. et al., Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Biochem.Biophys.Res.Commun. (2022)

Release Date

2022-12-21

Peptides

Ricin A chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ricin A chain

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