MolNFT v1 · #118685 · protein

Structure of HLA-A2:01 with peptide Y9L

5F9J · HLA class I histocompatibility antigen, a-2 alpha chain: “Structure of HLA-A2:01 with peptide Y9L”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #118685 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5F9J
Type: protein
Length: 381 residues
Chains: 3
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; Peptide Y9L
UniProt: P01892, P61769
Pockets: 4 · best druggability 0.68

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	274	27% helix, 40% strand	P01892
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769
C	Peptide Y9L	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

4 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	585	0.68	0.77	53	GOL
2	140	0.50	0.79	23	GOL
3	105	0.41	0.77	20	empty
4	65	0.31	0.75	15	empty

Interfaces

2 interfaces between chains.

A–B · 1248 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 841 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5F9J · Structure of HLA-A2:01 with peptide Y9L · 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 0.98

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 5F9J · PDBe 5F9J · UniProt P01892 · UniProt P61769

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