SMTL ID : 8tfh.1

Ricin in complex with Fab JB4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

hetero-1-1-1-1-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: 3 residues within 4Å: Chain A: I.5, I.6, N.7 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: W.93, N.95, Y.125, L.227 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.93 NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: A.224, P.226, Y.240 Chain B: I.10, T.43, L.48, N.135 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.10

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

EDO.4: 4 residues within 4Å: Chain A: G.128, N.129, L.130, N.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.128, A:N.129, A:L.130 EDO.7: 2 residues within 4Å: Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) EDO.9: 2 residues within 4Å: Chain C: S.25, G.26 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.26

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

CL.5: 3 residues within 4Å: Chain A: V.15, R.190 Chain B: Y.148 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain D: D.28, R.69 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain D: T.181, D.183, R.187 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain B: N.113, S.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.114 SO4.8: 4 residues within 4Å: Chain C: T.28, F.29, S.30, N.77 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.29, C:S.30, C:N.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vance, D.J. et al., Structural Basis of Antibody-Mediated Inhibition of Ricin Toxin Attachment to Host Cells. Biochemistry (2023)

Release Date

2024-04-17

Peptides

Ricin A chain: A
Ricin B chain: B
JB4 monoclonal antibody heavy chain: C
JB4 monoclonal antibody light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Ricin A chain

Ricin B chain

JB4 monoclonal antibody heavy chain

JB4 monoclonal antibody light chain

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