SMTL ID : 7th2.1 (1 other biounit)

Single-domain VHH intrabodies neutralize ricin toxin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: I.11, N.12 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: F.110, T.111, V.113, R.116 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: E.210, W.213, G.214 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: H.96, P.97, N.99 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: G.133, N.134, L.135 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.50, T.79, N.80 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.236, R.237, N.238 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: R.41, H.42 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: T.192, R.193, Y.196, R.198 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: F.36, R.44, E.45, T.106, G.108 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: G.41, K.42, E.43 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.10: 4 residues within 4Å: Chain A: Y.93, Y.117, Y.156, S.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.93

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

SO4.13: 3 residues within 4Å: Chain B: V.12, Q.13, G.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.13, B:Q.13 Water bridges: B:S.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czajka, T.F. et al., Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins. J.Biol.Chem. (2022)

Release Date

2022-10-12

Peptides

Ricin A chain: A
VHH antibody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Ricin A chain

VHH antibody

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