MolNFT v1 · #158801 · protein

Structure of HLA-A2:01 with peptide MM96

6O53 · MHC class I antigen: “Structure of HLA-A2:01 with peptide MM96”. X-ray diffraction, 2 ligands (NA, SO4), 4 pockets (best druggability 0.69). MolNFT v1 #158801 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6O53
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; MM96
UniProt: U5YJM1, P61769
Ligands: NA, SO4
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	273	26% helix, 41% strand	U5YJM1
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	MM96	protein	10	0% helix, 0% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	629	0.69	0.77	54	GOL
2	76	0.42	0.80	15	GOL
3	60	0.39	0.80	16	empty
4	81	0.35	0.76	16	empty

Interfaces

2 interfaces between chains.

A–B · 1306 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 801 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6O53 · Structure of HLA-A2:01 with peptide MM96 · the same entry in another collection · chain A against A, 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 0.99

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 U5YJM1
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6O53 · PDBe 6O53 · UniProt U5YJM1 · UniProt P61769

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