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Immune receptor

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

PDB: 1YPZ
Type: protein
Length: 1,598 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H2-T22 protein; Beta-2-microglobulin; T cell receptor delta; T-cell receptor gamma chain
UniProt: P61769
Ligands: NAG, MAN, FUC
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	H2-T22 protein	protein	260	15% helix, 35% strand	—
B, D	Beta-2-microglobulin	protein	102	0% helix, 46% strand	P61769
E, G	T cell receptor delta	protein	207	1% helix, 52% strand	—
F, H	T-cell receptor gamma chain	protein	230	8% helix, 43% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains E, F, G, H
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains F, H
FUC · alpha-L-fucopyranose · sugar · chains G

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	969	0.70	0.75	91	empty
2	599	0.69	0.78	51	empty
3	479	0.68	0.79	62	empty
4	595	0.67	0.77	48	empty
5	426	0.65	0.78	51	empty

Interfaces

12 interfaces between chains.

E–F · 1838 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 1751 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1373 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1354 Å² buried · 21 hydrogen bonds · protein-protein
C–G · 930 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 6 glycan (disulfide, N-glycosylation, glycosylation).

Compared structures

1YPZ · Immune receptor · the same entry in another collection · chain G against G, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P61769
Elsewhere: RCSB PDB 1YPZ · PDBe 1YPZ · UniProt P61769

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