Research workbench

HLA-C*06:02 presenting VRSRR(ABA)LRL

Analyse HLA-C*06:02 presenting VRSRR(ABA)LRL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W67
Type: protein
Length: 381 residues
Chains: 3
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: 4 · best druggability 0.65

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, cw-6 alpha chain	protein	273	27% helix, 40% strand	Q29963
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Val-arg-ser-arg-arg-aba-leu-arg-leu	protein	9	0% helix, 0% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C

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	525	0.65	0.77	52	empty
2	147	0.47	0.77	31	empty
3	50	0.42	0.83	17	empty
4	54	0.29	0.75	17	empty

Interfaces

2 interfaces between chains.

A–B · 1341 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 962 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

5W67 · HLA-C*06:02 presenting VRSRR(ABA)LRL · 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 0.99

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 5W67 · PDBe 5W67 · UniProt Q29963 · UniProt P61769

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