Research workbench

Ricin a chain bound to camelid nanobody (VHH5)

Analyse Ricin a chain bound to camelid nanobody (VHH5) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LHJ
Type: protein
Length: 378 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; Camelid antibody
EC: 3.2.2.22
UniProt: P02879
Ligands: CL
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ricin (EC 3.2.2.22)	protein	258	40% helix, 20% strand	P02879
B	Camelid antibody	protein	120	5% helix, 55% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	139	0.57	0.82	23	empty
2	245	0.56	0.78	36	empty

Interfaces

1 interface between chains.

A–B · 453 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4LHJ · Ricin A chain bound to camelid nanobody (VHH5) · 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 4LHJ · PDBe 4LHJ · UniProt P02879

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