Research workbench

Immune complex

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

PDB: 4Y1A
Type: protein
Length: 821 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
UniProt: P01903, P13760, P01308
Ligands: NAG
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dr alpha chain	protein	178	15% helix, 47% strand	P01903
B	HLA class II histocompatibility antigen, DRB1-4 beta chain	protein	184	18% helix, 43% strand	P13760
C	Insulin	protein	14	0% helix, 14% strand	P01308
D	FS17_ALPHA	protein	205	3% helix, 46% strand	—
E	FS17_BETA	protein	240	5% helix, 49% strand	—

Ligands and binding sites

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

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

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	286	0.71	0.85	38	empty
2	923	0.70	0.75	79	empty
3	171	0.49	0.77	26	empty
4	96	0.47	0.80	16	empty
5	114	0.46	0.79	20	empty

Interfaces

8 interfaces between chains.

A–B · 2470 Å² buried · 38 hydrogen bonds · protein-protein
D–E · 2171 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 654 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 644 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 280 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

4Y1A · immune complex · the same entry in another collection · chain A against A, TM-score 1.00
P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P01903
Every structure of UniProt P13760
Every structure of UniProt P01308
Elsewhere: RCSB PDB 4Y1A · PDBe 4Y1A · UniProt P01903 · UniProt P13760 · UniProt P01308

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