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Complex of the human MHC class II glycoprotein HLA-DR1 and the bacterial superantigen seb

Analyse Complex of the human MHC class II glycoprotein HLA-DR1 and the bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SEB
Type: protein
Length: 1,184 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen; Endogenous peptide model, poly-ala; Enterotoxin…
UniProt: P01903, P04229, P01552
Pockets: 16 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	HLA class II histocompatibility antigen	protein	181	14% helix, 45% strand	P01903
B, F	HLA class II histocompatibility antigen	protein	192	15% helix, 42% strand	P04229
C, G	Endogenous peptide model, poly-ala	protein	13	0% helix, 8% strand	—
D, H	Enterotoxin type B	protein	206	20% helix, 25% strand	P01552

Pockets

16 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	404	0.66	0.79	36	empty
2	289	0.55	0.76	37	empty
3	284	0.54	0.75	39	empty
4	153	0.52	0.79	26	empty
5	252	0.51	0.75	40	empty

Interfaces

12 interfaces between chains.

E–F · 2592 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 2561 Å² buried · 44 hydrogen bonds · protein-protein
A–D · 688 Å² buried · 11 hydrogen bonds · protein-protein
E–H · 685 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 480 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1SEB · Complex of the human MHC class II glycoprotein HLA-DR1 and the bacterial superantigen seb · the same entry in another collection · chain H against H, TM-score 1.00
P01552 · AlphaFold monomer V2.0 prediction for enterotoxin type B (P01552) · a predicted model of the same protein · chain D against A, TM-score 0.97
P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P01903
Every structure of UniProt P04229
Every structure of UniProt P01552
Elsewhere: RCSB PDB 1SEB · PDBe 1SEB · UniProt P01903 · UniProt P04229 · UniProt P01552

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