SMTL ID : 9e40.1

RTA-RUNT-202 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 01: 5-(4-fluoro-2,6-dimethylphenyl)thiophene-2-carboxylic acid

01.1: 9 residues within 4Å: Chain A: Y.187, L.236, R.238, R.239, F.244, V.246, I.251, L.252, I.255 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.187, A:L.236 Hydrogen bonds: A:R.239 Salt bridges: A:R.239 pi-Stacking: A:F.244

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 5 residues within 4Å: Chain A: C.263, A.264, P.266 Ligands: NI.9, CL.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.43 IMD.3: 2 residues within 4Å: Chain A: H.98 Ligands: NI.6 No protein-ligand interaction detected (PLIP) IMD.4: 3 residues within 4Å: Chain A: E.131, L.137 Ligands: NI.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.138

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 3 residues within 4Å: Chain A: Y.95, Y.119, Y.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.95

4 x NI: NICKEL (II) ION(Non-covalent)

NI.6: 2 residues within 4Å: Chain A: H.98 Ligands: IMD.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.98 NI.7: 3 residues within 4Å: Chain A: E.224, C.263 Ligands: NI.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.224, A:E.224, A:C.263 NI.8: 2 residues within 4Å: Chain A: R.138 Ligands: IMD.4 No protein-ligand interaction detected (PLIP) NI.9: 5 residues within 4Å: Chain A: C.263, A.264 Ligands: IMD.2, NI.7, CL.12 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.263, A:A.264

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: G.162, T.163, Q.164, T.167 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: Q.102, A.105, E.106 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: C.263, A.264 Ligands: IMD.2, NI.9 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: H.44 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLaughlin, J.E. et al., Binding of small molecules at the P-stalk site of ricin A subunit trigger conformational changes that extend into the active site. J.Biol.Chem. (2025)

Release Date

2025-05-14

Peptides

Ricin A chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ricin A chain

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