MolNFT v1 · #128310 · protein

HLA A02 presenting slfntiavl

5NMK · HLA class I histocompatibility antigen, a-2 alpha chain: “HLA A02 presenting slfntiavl”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.70). MolNFT v1 #128310 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5NMK
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; Gag protein
UniProt: P01892, P61769, W0GUW4
Ligands: SO4
Pockets: 6 · best druggability 0.70

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	276	26% helix, 40% strand	P01892
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Gag protein	protein	9	0% helix, 0% strand	W0GUW4

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C
GOL · Glycerol · additive · chains A

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	645	0.70	0.78	58	EDO
2	111	0.44	0.78	21	empty
3	54	0.42	0.82	17	EDO
4	59	0.33	0.77	16	empty
5	51	0.33	0.79	15	empty

Interfaces

2 interfaces between chains.

A–B · 1354 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 854 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5NMK · HLA A02 presenting SLFNTIAVL · 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
Every structure of UniProt W0GUW4
Elsewhere: RCSB PDB 5NMK · PDBe 5NMK · UniProt P01892 · UniProt P61769 · UniProt W0GUW4

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