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Structure of the mouse CD1D-4CLPHC-alpha-galcer-inkt TCR complex

Analyse Structure of the mouse CD1D-4CLPHC-alpha-galcer-inkt TCR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IRJ
Type: protein
Length: 804 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; VALPHA14 (mouse variable…
UniProt: P11609, P01887
Ligands: 1L9, NAG, FUC
Pockets: 9 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antigen-presenting glycoprotein CD1D1	protein	267	27% helix, 39% strand	P11609
B	Beta-2-microglobulin	protein	96	0% helix, 51% strand	P01887
C	VALPHA14 (mouse variable domain, human constant domain)	protein	202	4% helix, 48% strand	—
D	VBETA8.2 (mouse variable domain, human constant domain)	protein	239	6% helix, 49% strand	—

Ligands and binding sites

1L9 · N-[(2S,3S,4R)-1-({6-O-[(4-chlorophenyl)carbamoyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide · ligand · chains A, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
FUC · alpha-L-fucopyranose · sugar · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	907	0.86	0.87	77	1L9
2	333	0.62	0.78	44	empty
3	575	0.62	0.74	49	empty
4	219	0.49	0.75	29	empty
5	219	0.48	0.75	26	empty

Interfaces

4 interfaces between chains.

C–D · 2098 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1110 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 484 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 337 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

4IRJ · Structure of the mouse CD1d-4ClPhC-alpha-GalCer-iNKT TCR complex · the same entry in another collection · chain A against A, TM-score 1.00
P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 P11609
Every structure of UniProt P01887
Elsewhere: RCSB PDB 4IRJ · PDBe 4IRJ · UniProt P11609 · UniProt P01887

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