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Crystal structures of immune receptor complexes

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

PDB: 2PXY
Type: protein
Length: 608 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T cell receptor alpha chain; T cell receptor beta chain; H-2 class II histocompatibility…
UniProt: Q5R1F5, A2NTY6, P14438, P06344
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T cell receptor alpha chain	protein	114	3% helix, 51% strand	Q5R1F5
B	T cell receptor beta chain	protein	111	3% helix, 50% strand	A2NTY6
C	H-2 class II histocompatibility antigen, a-U alpha chain	protein	183	14% helix, 44% strand	P14438
D	H-2 class II histocompatibility antigen, a-U beta chain	protein	189	19% helix, 46% strand	P06344
P	Myelin basic protein (mbp)-peptide	protein	11	0% helix, 0% strand	—

Pockets

7 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	62	0.72	0.98	20	empty
2	315	0.58	0.77	41	empty
3	167	0.46	0.76	20	empty
4	121	0.43	0.77	23	empty
5	106	0.38	0.75	21	empty

Interfaces

10 interfaces between chains.

C–D · 2660 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 842 Å² buried · 15 hydrogen bonds · protein-protein
D–P · 628 Å² buried · 13 hydrogen bonds · protein-protein
C–P · 552 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 390 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

2PXY · Crystal structures of immune receptor complexes · the same entry in another collection · chain B against B, TM-score 1.00
P14438 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-U alpha… · a predicted model of the same protein · chain C against A, TM-score 0.97
P06344 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-U beta… · a predicted model of the same protein · chain D against A, TM-score 0.88

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 Q5R1F5
Every structure of UniProt A2NTY6
Every structure of UniProt P14438
Every structure of UniProt P06344
Elsewhere: RCSB PDB 2PXY · PDBe 2PXY · UniProt Q5R1F5 · UniProt A2NTY6 · UniProt P14438 · UniProt P06344

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