MolNFT v1 · #114794 · protein

HLA-A02 carrying ylggpdfpti

5C0E · HLA class I histocompatibility antigen, a-2 alpha chain: “HLA-A02 carrying ylggpdfpti”. X-ray diffraction, 1 ligand (BR), 4 pockets (best druggability 0.69). MolNFT v1 #114794 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5C0E
Type: protein
Length: 387 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: BR
Pockets: 4 · 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	277	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

BR · Bromide ion · ion · chains A
EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C
PG4 · Tetraethylene glycol · additive · 11 copies · chains A, C, B
GOL · Glycerol · additive · 4 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	641	0.69	0.78	57	EDO, GOL, PG4
2	83	0.42	0.79	22	PG4
3	64	0.42	0.81	18	PG4
4	50	0.27	0.75	17	PG4

Interfaces

2 interfaces between chains.

A–B · 1392 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 889 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5C0E · 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 0.99

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 5C0E · PDBe 5C0E · UniProt P01892 · UniProt P61769

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