MolNFT v1 · #156788 · protein

HLA-DQ2-glia-OMEGA1

6MFF · HLA class II histocompatibility antigen, dq alpha 1 chain: “HLA-DQ2-glia-OMEGA1”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.48). MolNFT v1 #156788 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MFF
Type: protein
Length: 372 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dq alpha 1 chain; MHC class II HLA-dq-beta-1…
UniProt: P01909, O19712
Ligands: NAG
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	180	14% helix, 44% strand	P01909
C	MHC class II HLA-dq-beta-1 - DQ2-glia-OMEGA1 chimeric protein	protein	192	19% helix, 42% strand	O19712

Ligands and binding sites

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

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	192	0.48	0.76	36	empty
2	118	0.38	0.74	22	empty
3	79	0.31	0.73	20	empty

Interfaces

1 interface between chains.

A–C · 2940 Å² buried · 56 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6MFF · HLA-DQ2-glia-omega1 · the same entry in another collection · chain A against A, 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 O19712
Elsewhere: RCSB PDB 6MFF · PDBe 6MFF · UniProt P01909 · UniProt O19712

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