MolNFT v1 · #98684 · protein

Ricin a chain bound to camelid nanobody (VHH3)

4LGR: “Ricin a chain bound to camelid nanobody (VHH3)”. X-ray diffraction, 2 ligands (ZN, CL), 3 pockets (best druggability 0.57). MolNFT v1 #98684 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4LGR
Type: protein
Length: 375 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; Camelid nanobody (VHH3)
EC: 3.2.2.22
UniProt: P02879
Ligands: ZN, CL
Pockets: 3 · 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	253	41% helix, 23% strand	P02879
B	Camelid nanobody (VHH3)	protein	122	5% helix, 49% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A, B
CL · Chloride ion · ion · 8 copies · chains A, B
ACY · Acetic acid · additive · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 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	284	0.57	0.77	32	empty
2	53	0.34	0.78	12	empty
3	75	0.32	0.74	21	EDO

Interfaces

1 interface between chains.

A–B · 725 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4LGR · Ricin A chain bound to camelid nanobody (VHH3) · 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 4LGR · PDBe 4LGR · UniProt P02879

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