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A structural basis for selection and cross-species reactivity of the semi-invariant nkt cell receptor in CD1D/GLYCOLIPID recognition

Analyse A structural basis for selection and cross-species reactivity of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EYR
Type: protein
Length: 443 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NKT12
UniProt: Q6PIZ8, Q2YDB4
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NKT12	protein	202	1% helix, 46% strand	Q6PIZ8
B	NKT12	protein	241	7% helix, 48% strand	Q2YDB4

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	962	0.73	0.76	82	empty
2	100	0.52	0.83	23	empty
3	57	0.32	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 2294 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

2EYR · A structural basis for selection and cross-species reactivity of the semi-invariant NKT… · 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 Q6PIZ8
Every structure of UniProt Q2YDB4
Elsewhere: RCSB PDB 2EYR · PDBe 2EYR · UniProt Q6PIZ8 · UniProt Q2YDB4

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