SMTL ID : 4hup.2 (1 other biounit)

Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanyl)-L-phenylalanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 19M: (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-3-phenyl-propanoic acid(Non-covalent)

19M.1: 14 residues within 4Å: Chain A: A.79, Y.80, V.81, F.93, G.121, N.122, Y.123, I.172, S.176, E.177, R.180, N.209, W.211, G.212 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.80 Hydrogen bonds: A:V.81, A:V.81, A:G.121, A:Y.123, A:S.176, A:R.180, A:R.180 Water bridges: A:D.124, A:E.208, A:G.212 pi-Stacking: A:Y.80, A:Y.123, A:W.211 pi-Cation interactions: A:Y.80 19M.6: 14 residues within 4Å: Chain B: A.79, Y.80, V.81, F.93, G.121, N.122, Y.123, I.172, S.176, E.177, R.180, N.209, W.211, G.212 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.80 Hydrogen bonds: B:V.81, B:V.81, B:G.121, B:Y.123, B:S.176, B:R.180, B:R.180 Water bridges: B:D.124, B:E.208, B:G.212 pi-Stacking: B:Y.80, B:Y.123, B:W.211 pi-Cation interactions: B:Y.80

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

SO4.2: 1 residues within 4Å: Chain A: H.65 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.65 Salt bridges: A:H.65 SO4.3: 3 residues within 4Å: Chain A: F.119, G.120, R.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.120 Water bridges: A:R.125 Salt bridges: A:R.125 SO4.7: 1 residues within 4Å: Chain B: H.65 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.65 Salt bridges: B:H.65 SO4.8: 3 residues within 4Å: Chain B: F.119, G.120, R.125 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.120 Water bridges: B:R.125 Salt bridges: B:R.125

4 x MLA: MALONIC ACID(Non-covalent)

MLA.4: 3 residues within 4Å: Chain A: N.195, R.196, R.197 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.195, A:R.197 Water bridges: A:G.142, A:E.146, A:E.146, A:E.146 Salt bridges: A:R.197, A:R.197 MLA.5: 4 residues within 4Å: Chain A: G.212, R.213, T.216, R.258 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.213 Hydrogen bonds: A:T.216 Water bridges: A:R.258 Salt bridges: A:R.213, A:R.213, A:R.258 MLA.9: 3 residues within 4Å: Chain B: N.195, R.196, R.197 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.195, B:R.197 Water bridges: B:G.142, B:R.197, B:R.197 Salt bridges: B:R.197, B:R.197 MLA.10: 4 residues within 4Å: Chain B: G.212, R.213, T.216, R.258 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.213 Water bridges: B:R.258 Salt bridges: B:R.213, B:R.213, B:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saito, R. et al., Peptide-conjugated pterins as inhibitors of ricin toxin A. J.Med.Chem. (2013)

Release Date

2012-12-26

Peptides

Ricin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

Ricin

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