SMTL ID : 6obo.1 (1 other biounit)

Ricin A chain bound to VHH antibody V6A6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 5 residues within 4Å: Chain B: T.56, Y.58 Ligands: ACY.2, ACY.3, CA.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.58 Hydrogen bonds: B:T.56 ACY.2: 4 residues within 4Å: Chain B: T.56 Ligands: ACY.1, ACY.3, CA.4 No protein-ligand interaction detected (PLIP) ACY.3: 6 residues within 4Å: Chain B: G.54, R.55, T.56 Ligands: ACY.1, ACY.2, CA.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.56

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain B: T.56 Ligands: ACY.1, ACY.2, ACY.3 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Ligand interactions Metal complexes: B:T.56, B:T.56, ACY.1, ACY.2, ACY.3

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

EDO.5: 6 residues within 4Å: Chain B: R.18, T.67, I.68, S.69, S.78, Q.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.67, B:S.78, B:Q.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.J. et al., Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site. J.Mol.Biol. (2020)

Release Date

2020-04-01

Peptides

Ricin A chain: A
VHH antibody V6A6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Ricin A chain

VHH antibody V6A6

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