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Crystal structure of HLA Class I antigen

Analyse Crystal structure of HLA Class I antigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XS3
Type: protein
Length: 378 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.5
Source: Homo sapiens
Molecule: Heavy Chain; Light Chain; P
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · resolution 2.5 · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heavy Chain	protein	271	27% helix, 41% strand	—
B	Light Chain	protein	98	0% helix, 50% strand	—
C	P	protein	9	0% helix, 0% strand	—

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	547	0.67	0.77	50	empty
2	165	0.44	0.75	34	empty
3	81	0.35	0.75	18	empty
4	66	0.29	0.74	14	empty

Interfaces

2 interfaces between chains.

A–B · 1253 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 959 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5XS3 · Crystal structure of HLA class I antigen · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 5XS3 · PDBe 5XS3

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