MolNFT v1 · #10968 · protein
Crystal structure of a complex of a human ALPHA/BETA-T cell receptor, influenza ha antigen peptide, and MHC class II molecule, HLA-DR4
1J8H · HLA class II histocompatibility antigen, dr alpha chain: “Crystal structure of a complex of a human ALPHA/BETA-T cell receptor, influenza ha antigen peptide, and MHC…”. X-ray diffraction, 2 ligands (NAG, NDG), 7 pockets (best…
- 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.
| Volume (ų) | 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 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 2015 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 716 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 698 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 412 Ų 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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