Research workbench

A2 HLA complex with L8A heteroclitic variant of melanoma peptide

Analyse A2 HLA complex with L8A heteroclitic variant of melanoma peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JFQ
Type: protein
Length: 771 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; L8A…
UniProt: P01892, P61769
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	28% helix, 40% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	L8A heteroclitic melanoma peptide	protein	10	0% helix, 0% strand	—
D	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	27% helix, 39% strand	P01892

Ligands and binding sites

GOL · Glycerol · additive · 19 copies · chains A, D, B, E
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, D

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1146	0.77	0.79	102	GOL
2	815	0.73	0.78	80	GOL
3	175	0.54	0.79	31	GOL
4	173	0.53	0.79	32	GOL
5	139	0.46	0.77	24	empty

Interfaces

5 interfaces between chains.

D–E · 1433 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1427 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 848 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 841 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 624 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4JFQ · A2 HLA complex with L8A 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 4JFQ · PDBe 4JFQ · UniProt P01892 · UniProt P61769

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