MolNFT v1 · #21426 · protein

Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide

1S9V · HLA class II histocompatibility antigen, DQ(3) alpha chain: “Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide”. X-ray diffraction, 9 pockets (best druggability 0.48). MolNFT v1 #21426 on GenesisL1: 3D…

PDB: 1S9V
Type: protein
Length: 739 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, DQ(3) alpha chain; HLA class II…
UniProt: P01909, P01918
Pockets: 9 · best druggability 0.48

Structure

x-ray diffraction · 5 distinct chains · 17% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, DQ(3) alpha chain	protein	179	15% helix, 44% strand	P01909
B	HLA class II histocompatibility antigen, DQ(1) beta chain	protein	181	20% helix, 45% strand	P01918
C, F	Alpha-I gliadin	protein	11	0% helix, 0% strand	—
D	HLA class II histocompatibility antigen, DQ(3) alpha chain	protein	177	14% helix, 44% strand	P01909
E	HLA class II histocompatibility antigen, DQ(1) beta chain	protein	180	21% helix, 46% strand	P01918

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B, D, F

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

Pockets

9 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	215	0.48	0.75	36	empty
2	97	0.46	0.80	23	empty
3	167	0.43	0.75	32	empty
4	152	0.42	0.74	24	empty
5	122	0.40	0.75	21	empty

Interfaces

7 interfaces between chains.

D–E · 2523 Å² buried · 47 hydrogen bonds · protein-protein
A–B · 2522 Å² buried · 49 hydrogen bonds · protein-protein
E–F · 615 Å² buried · 6 hydrogen bonds · protein-protein
D–F · 556 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 539 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1S9V · Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide · the same entry in another collection · chain F against F, 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 D 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 P01918
Elsewhere: RCSB PDB 1S9V · PDBe 1S9V · UniProt P01909 · UniProt P01918

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