Research workbench

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: 2UWE
Type: protein
Length: 1,630 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: HOMO SAPIENS; MUS MUSCULUS; SYNTHETIC CONSTRUCT
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
UniProt: P01892, P61769, Q9NPA0
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · resolution 2.4 · 5 distinct chains · 12% helix, 45% 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, 51% strand	P61769
C, J	Uncharacterized protein C15ORF24	protein	9	0% helix, 0% strand	Q9NPA0
E, L	Ahiii TCR alpha chain	protein	194	2% helix, 41% strand	—
F, M	Ahiii TCR beta chain	protein	237	8% helix, 52% strand	—

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1194	0.74	0.77	83	empty
2	1178	0.73	0.76	82	empty
3	758	0.71	0.77	70	empty
4	656	0.70	0.78	57	empty
5	472	0.64	0.77	40	empty

Interfaces

18 interfaces between chains.

E–F · 2286 Å² buried · 33 hydrogen bonds · protein-protein
L–M · 2222 Å² buried · 35 hydrogen bonds · protein-protein
H–I · 1437 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1378 Å² buried · 23 hydrogen bonds · protein-protein
H–J · 864 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

2UWE · Large CDR3A loop alteration as a function of MHC mutation · the same entry in another collection · chain M against M, 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 0.98

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
Every structure of UniProt Q9NPA0
Elsewhere: RCSB PDB 2UWE · PDBe 2UWE · UniProt P01892 · UniProt P61769 · UniProt Q9NPA0

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