MolNFT v1 · #10026 · protein

Histocompatibility antigen

1IEA · MHC class II I-ek: “Histocompatibility antigen”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.82). MolNFT v1 #10026 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1IEA
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, Q31163
Ligands: NAG
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	MHC class II I-ek	protein	182	14% helix, 47% strand	P01904
B, D	MHC class II I-ek	protein	214	15% helix, 41% strand	Q31163

Ligands and binding sites

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

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	513	0.82	0.88	74	empty
2	307	0.75	0.87	29	empty
3	365	0.74	0.85	32	empty
4	156	0.69	0.89	33	empty
5	73	0.58	0.89	23	empty

Interfaces

6 interfaces between chains.

C–D · 3370 Å² buried · 66 hydrogen bonds · protein-protein
A–B · 3349 Å² buried · 67 hydrogen bonds · protein-protein
B–D · 877 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 205 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 196 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1IEA · 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 Q31163
Elsewhere: RCSB PDB 1IEA · PDBe 1IEA · UniProt P01904 · UniProt Q31163

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