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Crystal structure of a complex of a human ALPHA/BETA-T cell receptor, influenza ha antigen peptide, and MHC class II molecule, HLA-DR4

Analyse Crystal structure of a complex of a human ALPHA/BETA-T cell receptor, influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1J8H
Type: protein
Length: 812 residues
Chains: 5
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, P13760, P03437
Ligands: NAG, NDG
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dr alpha chain	protein	180	13% helix, 47% strand	P01903
B	HLA class II histocompatibility antigen, dr-4 beta chain	protein	180	19% helix, 46% strand	P13760
C	Hemagglutinin HA1 peptide chain	protein	13	0% helix, 15% strand	P03437
D	T-cell receptor alpha chain	protein	198	6% helix, 42% strand	—
E	T-cell receptor beta chain	protein	241	7% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	886	0.74	0.78	67	empty
2	103	0.66	0.90	27	empty
3	130	0.47	0.78	17	empty
4	100	0.37	0.75	18	empty
5	105	0.36	0.74	32	empty

Interfaces

10 interfaces between chains.

A–B · 2471 Å² buried · 43 hydrogen bonds · protein-protein
D–E · 2015 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 716 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 698 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 412 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

1J8H · Crystal Structure of a Complex of a Human alpha/beta-T cell Receptor, Influenza HA… · 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 P13760
Every structure of UniProt P03437
Elsewhere: RCSB PDB 1J8H · PDBe 1J8H · UniProt P01903 · UniProt P13760 · UniProt P03437

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