Research workbench

HLA-A02 carrying ylggpdfpti

Analyse HLA-A02 carrying ylggpdfpti in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C0G
Type: protein
Length: 386 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; Marker…
UniProt: P01892, P61769
Ligands: SO4
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	26% helix, 40% strand	P01892
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Marker peptide	protein	10	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A
EDO · 1,2-ethanediol · additive · 14 copies · chains A, B

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

Pockets

6 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	633	0.69	0.77	60	EDO
2	97	0.50	0.82	21	empty
3	91	0.45	0.80	18	EDO
4	62	0.41	0.81	17	EDO
5	66	0.32	0.75	15	empty

Interfaces

2 interfaces between chains.

A–B · 1366 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 787 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5C0G · HLA-A02 carrying YLGGPDFPTI · 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 5C0G · PDBe 5C0G · UniProt P01892 · UniProt P61769

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