MolNFT v1 · #55848 · protein

Structure of new antigen receptor variable domain from sharks

2YWY: “Structure of new antigen receptor variable domain from sharks”. X-ray diffraction, 5 pockets (best druggability 0.58). MolNFT v1 #55848 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YWY
Type: protein
Length: 432 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: New antigen receptor variable domain
UniProt: A9CBG4
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	New antigen receptor variable domain	protein	113	3% helix, 56% strand	A9CBG4
B, D	New antigen receptor variable domain	protein	103	3% helix, 59% strand	A9CBG4

Pockets

5 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	74	0.58	0.89	23	empty
2	52	0.53	0.89	21	empty
3	251	0.52	0.75	33	empty
4	93	0.44	0.79	16	empty
5	76	0.35	0.76	16	empty

Interfaces

3 interfaces between chains.

A–C · 948 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 623 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 609 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2YWY · Structure of new antigen receptor variable domain from sharks · 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 A9CBG4
Elsewhere: RCSB PDB 2YWY · PDBe 2YWY · UniProt A9CBG4

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