Research workbench

S2 protein complex

Analyse S2 protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OZI
Type: protein
Length: 1,629 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: 19 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	181	11% helix, 44% strand	P01909
B	HLA class II histocompatibility antigen, dq beta 1 chain	protein	180	19% helix, 42% strand	Q5Y7D3
D	HLA class II histocompatibility antigen, dq beta 1 chain	protein	181	18% helix, 43% strand	Q5Y7D3
E, G	T-cell receptor, S2, alpha chain	protein	199	2% helix, 40% strand	—
F, H	T-cell receptor, S2, beta chain	protein	243	7% helix, 49% strand	—
I, J	Deamidated gliadin-ALPHA1 peptide	protein	11	0% helix, 0% strand	—

Ligands and binding sites

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

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

Pockets

19 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	94	0.77	0.98	27	empty
2	86	0.76	0.98	18	empty
3	1007	0.71	0.75	75	empty
4	1105	0.71	0.75	93	empty
5	179	0.48	0.76	27	empty

Interfaces

21 interfaces between chains.

A–B · 2659 Å² buried · 48 hydrogen bonds · protein-protein
C–D · 2597 Å² buried · 47 hydrogen bonds · protein-protein
E–F · 2225 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 2154 Å² buried · 21 hydrogen bonds · protein-protein
B–J · 698 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4OZI · S2 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 0.95

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

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