SMTL ID : 7kd0.1

Ricin bound to VHH antibody V2C11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.1: 4 residues within 4Å: Chain A: I.8, I.9, N.10, R.31 No protein-ligand interaction detected (PLIP)

2 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.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 NAG-NAG-BMA.3: 9 residues within 4Å: Chain A: F.226, A.227, P.229, Y.243 Chain B: I.10, V.11, T.43, L.48, N.135 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.10

2 x GAL: beta-D-galactopyranose(Post Translational Modification)(Non-covalent)

GAL.4: 6 residues within 4Å: Chain A: D.124, E.127, L.133, R.134, E.135, N.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.124 Water bridges: A:Y.123 Salt bridges: A:R.134 GAL.13: 8 residues within 4Å: Chain B: D.22, V.23, R.24, D.25, Q.35, W.37, K.40, N.46 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.22, B:D.25, B:D.25, B:G.26, B:Q.35, B:Q.35, B:K.40, B:K.40, B:N.46

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

EDO.5: 5 residues within 4Å: Chain A: I.104, T.105, R.114, Y.115, T.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.114, A:R.114 Water bridges: A:A.101 EDO.6: 4 residues within 4Å: Chain A: E.127, Q.128, G.131, L.133 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 2 residues within 4Å: Chain A: E.102, H.106 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.102, A:E.102, A:H.106, H2O.3

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

CL.8: 4 residues within 4Å: Chain A: Y.243, D.244 Chain B: T.134, N.136 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: H.94 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: T.105, H.106 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: P.52, I.53 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: V.256 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: A.83, A.84 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
Anti-RON nanobody: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ricin chain A

Ricin chain B

Anti-RON nanobody

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