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Large CDR3A loop alteration as a function of MHC mutation.

Analyse Large CDR3A loop alteration as a function of MHC mutation. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2J8U
Type: protein
Length: 1,630 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
UniProt: P01892, P61769
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 40% strand	P01892
B, I	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, J	Self-peptide P1049	protein	9	0% helix, 0% strand	—
E, L	Ahiii TCR alpha chain	protein	194	4% helix, 39% strand	—
F, M	Ahiii TCR beta chain	protein	237	6% helix, 53% strand	—

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	850	0.78	0.81	83	empty
2	898	0.75	0.79	75	empty
3	794	0.72	0.78	70	empty
4	647	0.70	0.78	54	empty
5	163	0.53	0.79	28	empty

Interfaces

19 interfaces between chains.

E–F · 2267 Å² buried · 30 hydrogen bonds · protein-protein
L–M · 2251 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1444 Å² buried · 20 hydrogen bonds · protein-protein
H–I · 1432 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 846 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

2J8U · Large CDR3a loop alteration as a function of MHC mutation. · the same entry in another collection · chain E against E, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain I 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 P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 2J8U · PDBe 2J8U · UniProt P01892 · UniProt P61769

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