Research workbench

Nanobody targeting human VSIG4 in spacegroup C2

Analyse Nanobody targeting human VSIG4 in spacegroup C2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IMK
Type: protein
Length: 243 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nanobody; V-set and immunoglobulin domain-containing protein 4
UniProt: Q9Y279
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Nanobody	protein	125	10% helix, 47% strand	—
A	V-set and immunoglobulin domain-containing protein 4	protein	118	5% helix, 53% strand	Q9Y279

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.37	0.78	12	empty

Interfaces

1 interface between chains.

B–A · 801 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5IMK · Nanobody targeting human Vsig4 in Spacegroup C2 · the same entry in another collection · chain B against B, TM-score 1.00
Q9Y279 · AlphaFold monomer V2.0 prediction for V-set and immunoglobulin domain-containing protein… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9Y279
Elsewhere: RCSB PDB 5IMK · PDBe 5IMK · UniProt Q9Y279

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.