SMTL ID : 7th2.2 (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

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

CL.1: 3 residues within 4Å: Chain A: R.236, R.237, N.238 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: A.16, G.17, H.67 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: N.25, R.28, A.29 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: N.124, Y.125, D.126 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: N.238 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: H.42, G.226, V.247, S.248, I.251 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: P.5, D.112 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.28 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.13: 2 residues within 4Å: Chain B: R.44, Y.94 Ligand excluded by PLIP

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

SO4.10: 4 residues within 4Å: Chain A: F.121, G.122, N.124, R.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.122, A:N.124 Water bridges: A:R.127 Salt bridges: A:R.127 SO4.11: 8 residues within 4Å: Chain A: K.6, Q.7, Y.8, L.61, H.108, L.109, F.110, T.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.8, A:F.110, A:T.111

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

MES.12: 1 residues within 4Å: Chain A: I.3 No protein-ligand interaction detected (PLIP)

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

EDO.14: 4 residues within 4Å: Chain B: R.66, S.84, L.85, K.86 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.84 Water bridges: B:K.86 EDO.15: 4 residues within 4Å: Chain B: T.57, Y.59, T.68, I.69 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.57, B:T.57, B:Y.59

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
B

B
D

Ricin A chain

VHH antibody

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