SMTL ID : 6urx.1

Crystal structure of ricin A chain in complex with inhibitor 5-phenyl-2-thiophenecarboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 1 residues within 4Å: Chain A: R.190 Ligand excluded by PLIP EDO.2: 1 residues within 4Å: Chain A: P.163 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: E.62, S.70, V.71, T.72, R.86, A.87, G.88 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: Y.184, G.187, E.188 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: I.248, P.251, I.252 Ligands: EDO.10, JMG.16 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: E.147, A.148, T.164, R.167, S.168, I.171 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: V.39, H.41, I.43, P.44 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: Q.183, I.250 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: Q.161, L.162, P.163 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: R.235, F.241 Ligands: EDO.5, JMG.16 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Q.6, E.62, T.72, R.86, F.109 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: F.93, I.105, T.106, R.115, T.117 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: G.213, R.214, R.259 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: Q.129 Ligands: DMS.17 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Y.116, F.118, Y.155 Ligand excluded by PLIP

1 x JMG: 5-phenylthiophene-2-carboxylic acid(Non-covalent)

JMG.16: 9 residues within 4Å: Chain A: Y.184, L.233, Q.234, R.235, R.236, F.241, I.252 Ligands: EDO.5, EDO.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.184, A:L.233, A:I.252, A:I.252 Hydrogen bonds: A:R.236 Water bridges: A:R.236, A:N.237 Salt bridges: A:R.236 pi-Stacking: A:F.241

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.17: 2 residues within 4Å: Chain A: Q.129 Ligands: EDO.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X.P. et al., Small Molecule Inhibitors Targeting the Interaction of Ricin Toxin A Subunit with Ribosomes. Acs Infect Dis. (2020)

Release Date

2020-06-17

Peptides

Ricin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ricin

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