Research workbench

S16 protein complex

Analyse S16 protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OZH
Type: protein
Length: 1,619 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dq alpha 1 chain; HLA class II…
UniProt: P01909, Q5Y7D3
Ligands: NAG, CA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	181	14% helix, 44% strand	P01909
B, D	HLA class II histocompatibility antigen, dq beta 1 chain	protein	181	19% helix, 45% strand	Q5Y7D3
E, G	T-cell receptor, S16, alpha chain	protein	195	2% helix, 42% strand	—
F, H	T-cell receptor, S16, beta chain	protein	240	7% helix, 49% strand	—
I	Gliadin-ALPHA2 peptide	protein	12	0% helix, 0% strand	—
J	Gliadin-ALPHA2 peptide	protein	13	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C
CA · Calcium ion · metal · chains G

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

Pockets

20 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	903	0.79	0.82	110	empty
2	847	0.78	0.81	80	empty
3	162	0.60	0.83	36	empty
4	209	0.57	0.79	32	empty
5	113	0.47	0.79	23	empty

Interfaces

24 interfaces between chains.

C–D · 2638 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 2590 Å² buried · 49 hydrogen bonds · protein-protein
G–H · 2089 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2088 Å² buried · 22 hydrogen bonds · protein-protein
A–J · 671 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

4OZH · S16 protein complex · the same entry in another collection · chain J against J, TM-score 1.00
P01909 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dq alpha 1… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P01909
Every structure of UniProt Q5Y7D3
Elsewhere: RCSB PDB 4OZH · PDBe 4OZH · UniProt P01909 · UniProt Q5Y7D3

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