MolNFT v1 · #102881 · protein

D2 protein complex

4OZG · HLA class II histocompatibility antigen, dq alpha 1 chain: “D2 protein complex”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.74). MolNFT v1 #102881 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4OZG
Type: protein
Length: 1,615 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 0.74

Structure

x-ray diffraction · 8 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	181	14% helix, 44% strand	P01909
B	HLA class II histocompatibility antigen, dq beta 1 chain	protein	181	18% helix, 46% strand	Q5Y7D3
C	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	180	14% helix, 42% strand	P01909
D	HLA class II histocompatibility antigen, dq beta 1 chain	protein	180	18% helix, 46% strand	Q5Y7D3
E, G	T-cell receptor, D2, alpha chain	protein	194	2% helix, 42% strand	—
F, H	T-cell receptor, D2, beta chain	protein	240	7% helix, 49% strand	—
I	Deamidated gliadin-ALPHA2 peptide	protein	13	0% helix, 0% strand	—
J	Deamidated gliadin-ALPHA2 peptide	protein	12	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C
CA · Calcium ion · metal · chains C

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

Pockets

20 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	407	0.74	0.84	58	empty
2	410	0.72	0.83	61	empty
3	100	0.67	0.91	24	empty
4	58	0.54	0.88	23	empty
5	102	0.51	0.82	24	empty

Interfaces

23 interfaces between chains.

A–B · 2597 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 2586 Å² buried · 50 hydrogen bonds · protein-protein
G–H · 1933 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1894 Å² buried · 17 hydrogen bonds · protein-protein
C–I · 672 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4OZG · D2 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 4OZG · PDBe 4OZG · UniProt P01909 · UniProt Q5Y7D3

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