SMTL ID : 8tfl.1

Ricin in complex with Fab SylH3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NDG-NAG.1: 5 residues within 4Å: Chain B: W.92, D.93, N.94, Y.124, L.226 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.92 Hydrogen bonds: B:Y.124, B:Y.124 NDG-NAG.2: 8 residues within 4Å: Chain A: F.222, A.223, P.225, Y.239 Chain B: I.9, V.10, L.47, N.134 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.9, B:V.10, A:Y.239 Water bridges: B:I.9, B:I.9, A:A.223 Hydrogen bonds: B:I.9, B:N.134

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Post Translational Modification)

NDG.3: 3 residues within 4Å: Chain A: I.4, I.5, N.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.4

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.4: 6 residues within 4Å: Chain D: A.133, P.134, R.196, V.201, T.202, K.216 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.134, D:R.196

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
SylH3 Fab light chain: C
SylH3 Fab heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
L

D
H

Ricin A chain

Ricin B chain

SylH3 Fab light chain

SylH3 Fab heavy chain