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Ricin toxin in complex with neutralizing single chain monoclonal antibodies (vhhs)

Analyse Ricin toxin in complex with neutralizing single chain monoclonal antibodies… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E1H
Type: protein
Length: 382 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; F8(JOB10) vhh antibody
EC: 3.2.2.22
UniProt: P02879
Ligands: CL
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ricin (EC 3.2.2.22)	protein	258	42% helix, 23% strand	P02879
B	F8(JOB10) vhh antibody	protein	124	10% helix, 52% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	241	0.56	0.78	33	empty
2	51	0.35	0.79	14	empty
3	91	0.35	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 574 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5E1H · Ricin toxin in complex with neutralizing single chain monoclonal antibodies (VHHs) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P02879
Elsewhere: RCSB PDB 5E1H · PDBe 5E1H · UniProt P02879

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