Research workbench

XPA5 TCR in complex with HLA-DQ2-OMEGA1

Analyse XPA5 TCR in complex with HLA-DQ2-OMEGA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SG2
Type: protein
Length: 1,569 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; MHC class II HLA-dq-beta-1…
UniProt: P01909, O19712
Ligands: NAG, CA
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 9 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	178	15% helix, 43% strand	P01909
B	MHC class II HLA-dq-beta-1	protein	175	21% helix, 46% strand	O19712
F	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	178	15% helix, 46% strand	P01909
G	MHC class II HLA-dq-beta-1	protein	180	20% helix, 45% strand	O19712
D	T-cell receptor, XPA5, alpha chain	protein	188	3% helix, 43% strand	—
E	T-cell receptor, XPA5, beta chain	protein	242	6% helix, 48% strand	—
C, H	DQ2-glia-OMEGA1 peptide	protein	13	0% helix, 0% strand	—
I	T-cell receptor, XPA5, alpha chain	protein	170	4% helix, 45% strand	—
J	T-cell receptor, XPA5, beta chain	protein	232	4% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, F
CA · Calcium ion · metal · 2 copies · chains B, E
EDO · 1,2-ethanediol · additive · 3 copies · chains A, J
ACT · Acetate ion · additive · 2 copies · chains A, B, F

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	983	0.72	0.76	87	empty
2	944	0.70	0.75	84	empty
3	660	0.66	0.75	64	empty
4	369	0.56	0.74	48	empty
5	366	0.55	0.74	48	empty

Interfaces

24 interfaces between chains.

F–G · 2543 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 2536 Å² buried · 48 hydrogen bonds · protein-protein
D–E · 1977 Å² buried · 20 hydrogen bonds · protein-protein
I–J · 1826 Å² buried · 24 hydrogen bonds · protein-protein
B–G · 742 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7SG2 · XPA5 TCR in complex with HLA-DQ2-omega1 · 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 F against A, TM-score 0.97

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 7SG2 · PDBe 7SG2 · UniProt P01909 · UniProt O19712

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