Research workbench
Crystal structure of a complex of a human ALPHA/BETA-T cell receptor, influenza ha antigen peptide, and MHC class II molecule, HLA-DR1
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
- 1FYT
- Type
- protein
- Length
- 810 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, P04229, P03437, P01850
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 13% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, dr-1 beta chain | protein | 179 | 18% helix, 44% strand | P04229 |
| C | Hemagglutinin HA1 peptide chain | protein | 13 | 0% helix, 8% strand | P03437 |
| D | T-cell receptor alpha chain | protein | 198 | 7% helix, 44% strand | — |
| E | T-cell receptor beta chain | protein | 240 | 7% helix, 49% strand | P01850 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.75 | 0.78 | 75 | empty |
| 2 | 104 | 0.69 | 0.92 | 28 | empty |
| 3 | 157 | 0.45 | 0.76 | 23 | empty |
| 4 | 114 | 0.37 | 0.74 | 18 | empty |
| 5 | 79 | 0.36 | 0.76 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2541 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 2105 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 704 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 685 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 446 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1FYT · Crystal structure of a complex of a human ALPHA/BETA-T cell receptor, influenza ha… · the same entry in another collection · chain B against B, 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
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain E against A, TM-score 0.53
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 P03437
- Every structure of UniProt P01850
- Elsewhere: RCSB PDB 1FYT · PDBe 1FYT · UniProt P01903 · UniProt P04229 · UniProt P03437 · UniProt P01850
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