SMTL ID : 7tgf.1

Single-domain VHH intrabodies neutralize ricin toxin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: F.11, T.13, A.16, Y.21, G.140, N.141, L.144, M.174, M.188, I.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.140 Water bridges: A:I.192 EDO.9: 11 residues within 4Å: Chain B: F.37, A.97, T.98, E.99, T.103, G.105, G.108, H.109, G.110, D.113, W.115 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.108, B:G.110, B:W.115 Water bridges: B:G.108, B:H.109

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

CL.2: 4 residues within 4Å: Chain A: L.133, R.134, E.135, I.205 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: F.119, G.120, N.122, R.125 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: T.13, A.14, N.64, H.65, E.145 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: Y.115, F.117, A.118, F.119 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: R.48, T.77, N.78, V.256 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: T.190, R.191, R.196, S.198 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: P.46, Q.55, V.76 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: Q.182 Chain B: A.33, S.52, Y.59, V.101, C.102 Ligand excluded by PLIP

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 chain A: A
VHH camelid antibody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ricin chain A

VHH camelid antibody

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