Research workbench

Histocompatibility antigen

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

PDB: 1IEB
Type: protein
Length: 792 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class II I-ek
UniProt: P01904, Q31164
Ligands: NAG, SO4
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	MHC class II I-ek	protein	182	14% helix, 43% strand	P01904
B, D	MHC class II I-ek	protein	214	16% helix, 34% strand	Q31164

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · chains B, D

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

Pockets

5 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	1175	0.85	0.86	112	SO4
2	304	0.75	0.87	27	empty
3	303	0.74	0.86	28	empty
4	88	0.61	0.89	16	empty
5	68	0.29	0.73	18	empty

Interfaces

5 interfaces between chains.

C–D · 3454 Å² buried · 67 hydrogen bonds · protein-protein
A–B · 3443 Å² buried · 75 hydrogen bonds · protein-protein
B–D · 793 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 201 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 199 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

1IEB · Histocompatibility antigen · the same entry in another collection · chain A against A, TM-score 1.00
P01904 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, E-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P01904
Every structure of UniProt Q31164
Elsewhere: RCSB PDB 1IEB · PDBe 1IEB · UniProt P01904 · UniProt Q31164

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