Research workbench
Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one gm 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
- 6TDO
- Type
- protein
- Length
- 375 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin
- UniProt
- F6IQS1, P61769
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 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
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.67 | 0.77 | 59 | GOL |
| 2 | 79 | 0.42 | 0.80 | 19 | empty |
| 3 | 84 | 0.40 | 0.78 | 15 | empty |
| 4 | 61 | 0.37 | 0.79 | 18 | empty |
| 5 | 114 | 0.37 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1329 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6TDO · Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM… · 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 6TDO · PDBe 6TDO · UniProt F6IQS1 · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.