MolNFT v1 · #90399 · protein

Structure of XV19 VALPHA1-VBETA16 type-II natural killer T cell receptor

4EI6 · VALPHA1 XV19 type II natural killer T cell receptor (mouse…: “Structure of XV19 VALPHA1-VBETA16 type-II natural killer T cell receptor”. X-ray diffraction, 9 pockets (best druggability 0.69). MolNFT v1 #90399 on GenesisL1: 3D…

PDB: 4EI6
Type: protein
Length: 876 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VALPHA1 XV19 type II natural killer T cell receptor (mouse variable domain, human…
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VALPHA1 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain)	protein	202	5% helix, 47% strand	—
B	VBETA16 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain)	protein	244	7% helix, 50% strand	—
C	VALPHA1 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain)	protein	189	7% helix, 50% strand	—
D	VBETA16 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain)	protein	241	6% helix, 51% strand	—

Pockets

9 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	670	0.69	0.77	71	empty
2	480	0.65	0.77	62	empty
3	373	0.62	0.78	39	empty
4	127	0.49	0.79	34	empty
5	151	0.41	0.74	39	empty

Interfaces

3 interfaces between chains.

A–B · 2282 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2248 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 1016 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

4EI6 · Structure of XV19 Valpha1-Vbeta16 Type-II Natural Killer T cell receptor · 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
Elsewhere: RCSB PDB 4EI6 · PDBe 4EI6

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