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Human class II MHC protein HLA-DR1 bound to a designed peptide related to influenza virus hemagglutinin, FVKQNA(MAA)AL, in complex with staphylococcal enterotoxin C3 variant 3B2 (SEC3-3B2)

Analyse Human class II MHC protein HLA-DR1 bound to a designed peptide related to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PYW
Type: protein
Length: 608 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
UniProt: P01903, P13758, P23313
Ligands: ACE
Pockets: 7 · best druggability 0.48

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dr alpha chain	protein	179	14% helix, 46% strand	P01903
B	HLA class II histocompatibility antigen, dr-1 beta chain	protein	190	18% helix, 44% strand	P13758
C	9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL	protein	9	0% helix, 0% strand	—
D	Enterotoxin type C-3	protein	230	20% helix, 34% strand	P23313

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B, C

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

Pockets

7 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	172	0.48	0.76	22	empty
2	202	0.48	0.75	22	empty
3	56	0.42	0.83	21	empty
4	79	0.32	0.74	16	empty
5	66	0.28	0.73	19	empty

Interfaces

4 interfaces between chains.

A–B · 2527 Å² buried · 46 hydrogen bonds · protein-protein
A–D · 673 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 560 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 513 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nonstandard).

Compared structures

1PYW · Human class II MHC protein HLA-DR1 bound to a designed peptide related to influenza virus… · the same entry in another collection · chain A against A, TM-score 1.00
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 0.96

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 P01903
Every structure of UniProt P13758
Every structure of UniProt P23313
Elsewhere: RCSB PDB 1PYW · PDBe 1PYW · UniProt P01903 · UniProt P13758 · UniProt P23313

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