MolNFT v1 · #138023 · protein

HLA-C*06:02 presenting arfndlrfv

5W69 · HLA class I histocompatibility antigen, cw-6 alpha chain: “HLA-C*06:02 presenting arfndlrfv”. X-ray diffraction, 19 pockets (best druggability 0.73). MolNFT v1 #138023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5W69
Type: protein
Length: 1,523 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, cw-6 alpha chain; Beta-2-microglobulin…
UniProt: Q29963, P61769
Pockets: 19 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	HLA class I histocompatibility antigen, cw-6 alpha chain	protein	273	28% helix, 40% strand	Q29963
B, D, F, H	Beta-2-microglobulin	protein	100	0% helix, 50% strand	P61769
G	HLA class I histocompatibility antigen, cw-6 alpha chain	protein	268	29% helix, 39% strand	Q29963
I, J, K, L	Ala-arg-phe-asn-asp-leu-arg-phe-val	protein	9	0% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.73	0.77	97	empty
2	696	0.70	0.77	56	empty
3	375	0.68	0.81	47	empty
4	617	0.68	0.77	60	empty
5	367	0.67	0.81	53	empty

Interfaces

17 interfaces between chains.

C–D · 1423 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1378 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1352 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1321 Å² buried · 19 hydrogen bonds · protein-protein
C–J · 991 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5W69 · HLA-C*06:02 presenting ARFNDLRFV · the same entry in another collection · chain L against L, TM-score 1.00

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 Q29963
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5W69 · PDBe 5W69 · UniProt Q29963 · UniProt P61769

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