SMTL ID : 7kdu.1

Ricin bound to VHH antibody V5E4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain A: I.8, N.10, R.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.31, A:I.8, A:N.10

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.2: 4 residues within 4Å: Chain B: W.93, N.95, Y.125, L.227 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: F.226, A.227, P.229, Y.243 Chain B: I.10, T.43, L.48, N.135 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.10 Water bridges: A:A.227

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

EDO.4: 2 residues within 4Å: Chain A: S.246 Chain B: Y.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.246

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 2 residues within 4Å: Chain A: E.102, H.106 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.102, A:E.102, A:H.106 ZN.6: 3 residues within 4Å: Chain A: E.127, R.134, E.135 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.135, H2O.1, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.J. et al., Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin's A-B Subunit Interface. J.Mol.Biol. (2021)

Release Date

2021-08-04

Peptides

Ricin chain A: A
Ricin chain B: B
VHH antibody V5E4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ricin chain A

Ricin chain B

VHH antibody V5E4

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