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Shark ignar variable domain

Analyse Shark ignar variable domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HGK
Type: protein
Length: 1,172 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serum albumin; Shark V-nar antibody
UniProt: P02768
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 68% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serum albumin	protein	483	75% helix, 0% strand	P02768
B	Serum albumin	protein	481	75% helix, 0% strand	P02768
C, D	Shark V-nar antibody	protein	104	3% helix, 57% strand	—

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1148	0.85	0.86	96	empty
2	801	0.83	0.85	82	empty
3	769	0.80	0.83	74	empty
4	191	0.76	0.91	25	empty
5	202	0.76	0.90	25	empty

Interfaces

3 interfaces between chains.

B–C · 756 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 742 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 715 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

4HGK · Shark IgNAR variable domain · the same entry in another collection · chain A against A, TM-score 1.00
P02768 · AlphaFold monomer V2.0 prediction for albumin (P02768) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P02768
Elsewhere: RCSB PDB 4HGK · PDBe 4HGK · UniProt P02768

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