MolNFT v1 · #112002 · protein

S13 COMPLEX

4Z7U · MHC class II HLA-dq-alpha chain: “S13 COMPLEX”. X-ray diffraction, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.70). MolNFT v1 #112002 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Z7U
Type: protein
Length: 1,620 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class II HLA-dq-alpha chain; MHC class II HLA-dq-beta-1; T-cell receptor, S13 alpha…
UniProt: Q30069, O19707
Ligands: NAG, FUC
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 12% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	MHC class II HLA-dq-alpha chain	protein	182	14% helix, 45% strand	Q30069
B	MHC class II HLA-dq-beta-1	protein	169	21% helix, 43% strand	O19707
D	MHC class II HLA-dq-beta-1	protein	172	20% helix, 42% strand	O19707
E, G	T-cell receptor, S13 alpha chain	protein	198	5% helix, 42% strand	—
F, H	T-cell receptor, S13 beta chain	protein	244	7% helix, 50% strand	—
I	Deamidated DQ8-glia-ALPHA1 peptide	protein	15	0% helix, 7% strand	—
J	Deamidated DQ8-glia-ALPHA1 peptide	protein	16	0% helix, 6% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D, A, C
FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, D

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	981	0.70	0.74	96	empty
2	767	0.66	0.74	73	empty
3	345	0.55	0.74	53	empty
4	204	0.53	0.78	50	empty
5	190	0.53	0.78	41	empty

Interfaces

20 interfaces between chains.

C–D · 2605 Å² buried · 58 hydrogen bonds · protein-protein
A–B · 2604 Å² buried · 61 hydrogen bonds · protein-protein
E–F · 2127 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2123 Å² buried · 27 hydrogen bonds · protein-protein
D–I · 698 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4Z7U · S13 complex · the same entry in another collection · chain A against A, TM-score 1.00

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 Q30069
Every structure of UniProt O19707
Elsewhere: RCSB PDB 4Z7U · PDBe 4Z7U · UniProt Q30069 · UniProt O19707

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