MolNFT v1 · #127621 · protein

HLA-A02 carrying mvwgpdplyv

5N1Y · HLA class I histocompatibility antigen, a-2 alpha chain: “HLA-A02 carrying mvwgpdplyv”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #127621 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5N1Y
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; Mvwgpdplyv
UniProt: P01892, P61769
Pockets: 4 · best druggability 0.68

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	Mvwgpdplyv	protein	10	0% helix, 0% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
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	593	0.68	0.78	56	EDO, GOL
2	92	0.44	0.80	23	EDO
3	104	0.43	0.78	21	EDO
4	55	0.36	0.79	14	empty

Interfaces

2 interfaces between chains.

A–B · 1363 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 879 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5N1Y · HLA-A02 carrying MVWGPDPLYV · 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 5N1Y · PDBe 5N1Y · UniProt P01892 · UniProt P61769

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