Research workbench

Crystal structure of HLA-C*0501 in complex with sae

Analyse Crystal structure of HLA-C*0501 in complex with sae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VGD
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, cw-5 alpha chain; Beta-2-microglobulin…
UniProt: Q9TNN7, P61769
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, cw-5 alpha chain	protein	273	26% helix, 38% strand	Q9TNN7
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Ser-ala-glu-pro-val-pro-leu-gln-leu	protein	9	0% helix, 0% strand	—

Pockets

3 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	542	0.68	0.78	50	empty
2	75	0.43	0.81	21	empty
3	139	0.42	0.75	24	empty

Interfaces

2 interfaces between chains.

A–B · 1342 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 850 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5VGD · Crystal Structure of HLA-C*0501 in complex with SAE · 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 Q9TNN7
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5VGD · PDBe 5VGD · UniProt Q9TNN7 · UniProt P61769

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