Research workbench
Crystal structure of HTLV-1 tax peptide bound to human class I MHC HLA-A2 with the E63Q and K66A mutations in the heavy chain.
Analyse Crystal structure of HTLV-1 tax peptide bound to human class I MHC HLA-A2 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AV1
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61770, P14079
- Ligands
- SCN
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 29% helix, 39% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61770 |
| C, F | Trans-activating transcriptional regulatory peptide | protein | 9 | 0% helix, 0% strand | P14079 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · chains B
- GOL · Glycerol · additive · 23 copies · chains A, B, C, D, E, F
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 | 656 | 0.70 | 0.78 | 56 | GOL |
| 2 | 582 | 0.68 | 0.78 | 59 | GOL |
| 3 | 79 | 0.49 | 0.83 | 17 | GOL |
| 4 | 132 | 0.48 | 0.79 | 26 | empty |
| 5 | 128 | 0.46 | 0.78 | 26 | empty |
Interfaces
4 interfaces between chains.
- D–E · 1485 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1457 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 809 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 808 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2AV1 · Crystal structure of HTLV-1 TAX peptide Bound to Human Class I MHC HLA-A2 with the E63Q… · the same entry in another collection · chain F against F, TM-score 1.00
- P61770 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61770) · a predicted model of the same protein · chain E 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 P01892
- Every structure of UniProt P61770
- Every structure of UniProt P14079
- Elsewhere: RCSB PDB 2AV1 · PDBe 2AV1 · UniProt P01892 · UniProt P61770 · UniProt P14079
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