Research workbench

XPA5 TCR in complex with HLA-DQ2-ALPHA1

Analyse XPA5 TCR in complex with HLA-DQ2-ALPHA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SG1
Type: protein
Length: 1,572 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, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	180	13% helix, 44% strand	P01909
B	MHC class II HLA-dq-beta-1	protein	174	21% helix, 45% strand	O19712
F	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	181	13% helix, 43% strand	P01909
G	MHC class II HLA-dq-beta-1	protein	179	19% helix, 45% strand	O19712
D	T-cell receptor, XPA5, alpha chain	protein	193	3% helix, 40% strand	—
E	T-cell receptor, XPA5, beta chain	protein	244	5% helix, 48% strand	—
C, H	DQ2-glia-ALPHA1A peptide	protein	15	0% helix, 0% strand	—
I	T-cell receptor, XPA5, alpha chain	protein	156	2% helix, 42% strand	—
J	T-cell receptor, XPA5, beta chain	protein	235	4% helix, 51% 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 A, F, E
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, F, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1005	0.72	0.76	83	empty
2	1115	0.71	0.75	113	empty
3	166	0.51	0.78	30	EDO
4	151	0.48	0.78	27	empty
5	145	0.47	0.77	26	EDO

Interfaces

24 interfaces between chains.

A–B · 2643 Å² buried · 49 hydrogen bonds · protein-protein
F–G · 2635 Å² buried · 44 hydrogen bonds · protein-protein
D–E · 1986 Å² buried · 17 hydrogen bonds · protein-protein
I–J · 1658 Å² buried · 12 hydrogen bonds · protein-protein
B–G · 749 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7SG1 · XPA5 TCR in complex with HLA-DQ2-alpha1 · 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 O19712
Elsewhere: RCSB PDB 7SG1 · PDBe 7SG1 · UniProt P01909 · UniProt O19712

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.