SMTL ID : 7kd2.1

Ricin bound to VHH antibody V11B2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.9 Hydrogen bonds: A:I.8, A:N.10, 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, D.94, N.95, Y.125 No protein-ligand interaction detected (PLIP)

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 No protein-ligand interaction detected (PLIP)

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: G.15, H.65 No protein-ligand interaction detected (PLIP) ZN.5: 2 residues within 4Å: Chain A: R.134, E.135 No protein-ligand interaction detected (PLIP) ZN.9: 1 residues within 4Å: Chain B: H.29 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.29 ZN.14: 3 residues within 4Å: Chain C: S.29, D.99, H.105 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.29, C:D.99, C:H.105, H2O.7 ZN.15: 4 residues within 4Å: Chain B: P.240, S.241 Chain C: R.98, R.103 No protein-ligand interaction detected (PLIP)

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

CL.6: 2 residues within 4Å: Chain A: P.95, D.100 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: T.190, R.193 Chain B: G.149 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: H.94 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: Y.69, S.70 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: L.48, T.50, R.58, S.59, N.60 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.27, H.29 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: R.16, T.110, G.208, P.209 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: R.236 Chain C: E.46, L.47, E.60 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 V11B2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ricin chain A

Ricin chain B

VHH antibody V11B2

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