SMTL ID : 7kc9.1 (1 other biounit)

Ricin bound to VHH antibody V5G1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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, I.9, N.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.8, A:N.10 Water bridges: A:N.10

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

NAG-NAG.2: 5 residues within 4Å: Chain B: Q.91, W.93, N.95, Y.125, L.227 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.93

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.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 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.10

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: H.40 Chain B: D.94 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.94, B:D.94, H2O.11 ZN.5: 2 residues within 4Å: Chain A: R.134, E.135 No protein-ligand interaction detected (PLIP) ZN.6: 1 residues within 4Å: Chain A: H.94 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.94, H2O.1 ZN.7: 1 residues within 4Å: Chain B: H.29 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.29

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

CL.8: 6 residues within 4Å: Chain B: T.97, I.98, V.106, L.107, Q.129, W.131 Ligand excluded by PLIP

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 V5G1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ricin chain A

Ricin chain B

VHH antibody V5G1

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