SMTL ID : 7xzt.1

Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-D-tyrosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x I9P: (2R)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-(4-hydroxyphenyl)propanoic acid(Non-covalent)

I9P.1: 14 residues within 4Å: Chain A: A.86, Y.87, V.88, F.100, G.128, N.129, Y.130, R.141, I.179, S.183, E.184, R.187, E.215, N.216 16 PLIP interactions: 16 interactions with chain A 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:Y.87, A:Y.87, A:N.129, A:D.131, A:E.215 Salt bridges: A:R.141 pi-Stacking: A:Y.87, A:Y.87, A:Y.130

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: 4 residues within 4Å: Chain A: F.126, G.127, N.129, R.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.127 Water bridges: A:G.128 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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