MolNFT v1 · #96299 · protein

A2 HLA complex with E1A heteroclitic variant of melanoma peptide

4JFO · HLA class I histocompatibility antigen, a-2 alpha chain: “A2 HLA complex with E1A heteroclitic variant of melanoma peptide”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.73). MolNFT v1 #96299 on GenesisL1: 3D…

PDB: 4JFO
Type: protein
Length: 770 residues
Chains: 6
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; E1A…
UniProt: P01892, P61769
Ligands: SO4
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	28% helix, 39% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	E1A heteroclitic melanoma peptide	protein	10	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · 10 copies · chains A, B, D, E

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.73	0.76	89	GOL
2	603	0.68	0.77	59	GOL
3	151	0.49	0.78	24	empty
4	61	0.43	0.82	17	GOL
5	109	0.42	0.77	20	empty

Interfaces

6 interfaces between chains.

D–E · 1454 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1431 Å² buried · 22 hydrogen bonds · protein-protein
D–F · 855 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 842 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 307 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4JFO · A2 HLA complex with E1A heteroclitic variant of Melanoma peptide · the same entry in another collection · chain F against F, 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 4JFO · PDBe 4JFO · UniProt P01892 · UniProt P61769

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