Research workbench

Human class I MHC HLA-A2 in complex with avgsyvysv peptide

Analyse Human class I MHC HLA-A2 in complex with avgsyvysv peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7U21
Type: protein
Length: 768 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen, a-2 alpha chain; Beta-2-microglobulin; PGM5 peptide (465-473) (H5Y)
UniProt: A0A5B8RNS7, P61769
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	MHC class I antigen, a-2 alpha chain	protein	275	28% helix, 39% strand	A0A5B8RNS7
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	PGM5 peptide (465-473) (H5Y)	protein	9	0% helix, 0% strand	—

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1164	0.78	0.80	102	empty
2	733	0.73	0.79	75	empty
3	170	0.54	0.79	30	empty
4	165	0.54	0.80	31	empty
5	133	0.47	0.78	19	empty

Interfaces

6 interfaces between chains.

D–E · 1466 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1404 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 790 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 744 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 583 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7U21 · Human Class I MHC HLA-A2 in complex with AVGSYVYSV peptide · the same entry in another collection · chain F against F, 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 A0A5B8RNS7
Every structure of UniProt P61769
Elsewhere: RCSB PDB 7U21 · PDBe 7U21 · UniProt A0A5B8RNS7 · UniProt P61769

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