Research workbench
Crystal structure of a H5-specific CTL epitope variant derived from H5N1 influenza virus in complex with HLA-A*0201
Analyse Crystal structure of a H5-specific CTL epitope variant derived from H5N1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MGT
- Type
- protein
- Length
- 1,540 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.197
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, A-2 alpha chain; Beta-2-microglobulin; 10-meric…
- UniProt
- P01892, P61769, Q1WDM0
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.197 · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | HLA class I histocompatibility antigen, A-2 alpha chain | protein | 275 | 27% helix, 39% strand | P01892 |
| B, E, H, K | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F, I, L | 10-meric peptide from Hemagglutinin | protein | 10 | 0% helix, 0% strand | Q1WDM0 |
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.77 | 0.80 | 93 | empty |
| 2 | 1088 | 0.76 | 0.78 | 86 | empty |
| 3 | 773 | 0.71 | 0.77 | 72 | empty |
| 4 | 749 | 0.71 | 0.77 | 70 | empty |
| 5 | 334 | 0.58 | 0.77 | 38 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1456 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1449 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1445 Ų buried · 25 hydrogen bonds · protein-protein
- J–K · 1432 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 959 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3MGT · Crystal structure of a H5-specific ctl epitope variant derived from H5N1 influenza virus… · the same entry in another collection · chain L against L, TM-score 1.00
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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt Q1WDM0
- Elsewhere: RCSB PDB 3MGT · PDBe 3MGT · UniProt P01892 · UniProt P61769 · UniProt Q1WDM0
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