Research workbench

Structure of HLA-A2:01 with the 12-mer peptide F12K

Analyse Structure of HLA-A2:01 with the 12-mer peptide F12K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DDH
Type: protein
Length: 385 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; 12-mer…
UniProt: P01892, P61769
Pockets: 4 · best druggability 0.67

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, 41% strand	P01892
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	12-mer peptide F12K	protein	12	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 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	565	0.67	0.77	56	GOL
2	87	0.43	0.79	17	empty
3	61	0.33	0.76	15	empty
4	59	0.31	0.76	16	empty

Interfaces

2 interfaces between chains.

A–B · 1315 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 987 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5DDH · Structure of HLA-A2:01 with the 12-mer peptide F12K · 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 P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5DDH · PDBe 5DDH · UniProt P01892 · UniProt P61769

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