Research workbench
Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GL dipeptide in the A pocket.
Analyse Crystal structure of the disulfide engineered HLA-A0201 molecule in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TDP
- Type
- protein
- Length
- 375 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Homo sapiens
- Molecule
- MHC class I antigen; Beta-2-microglobulin
- UniProt
- F6IQS1, P61769
- Ligands
- NA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.4 · 2 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 26% helix, 40% strand | F6IQS1 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.69 | 0.77 | 57 | GOL |
| 2 | 95 | 0.47 | 0.81 | 22 | empty |
| 3 | 168 | 0.47 | 0.75 | 27 | GOL |
| 4 | 98 | 0.43 | 0.78 | 22 | empty |
| 5 | 89 | 0.39 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1304 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6TDP · Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one gl… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 F6IQS1
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6TDP · PDBe 6TDP · UniProt F6IQS1 · UniProt P61769
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