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Ricin a chain bound to camelid nanobody (VHH8)

Analyse Ricin a chain bound to camelid nanobody (VHH8) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LHQ
Type: protein
Length: 776 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; Camelid nanobody
EC: 3.2.2.22
UniProt: P02879
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Ricin (EC 3.2.2.22)	protein	260	37% helix, 23% strand	P02879
B, D	Camelid nanobody	protein	128	7% helix, 49% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	485	0.59	0.74	35	empty
2	303	0.58	0.77	34	empty
3	302	0.57	0.77	35	empty
4	57	0.40	0.80	11	empty
5	60	0.39	0.79	11	empty

Interfaces

3 interfaces between chains.

C–D · 551 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 548 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 249 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4LHQ · Ricin A chain bound to camelid nanobody (VHH8) · 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 4LHQ · PDBe 4LHQ · UniProt P02879

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