Research workbench
Human class I MHC HLA-A2 in complex with the modified HTLV-1 tax (Y5K- 4-[3-indolyl]-butyric acid) peptide
Analyse Human class I MHC HLA-A2 in complex with the modified HTLV-1 tax (Y5K… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GIT
- 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
- Q9TQH5, P61769
- Ligands
- NA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 27% helix, 39% strand | Q9TQH5 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Transcriptional activator tax | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- FMT · Formic acid · additive · 9 copies · chains B, A, C, D, E
- GOL · Glycerol · additive · 6 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.74 | 0.78 | 79 | GOL, FMT |
| 2 | 665 | 0.69 | 0.77 | 58 | GOL, FMT |
| 3 | 75 | 0.49 | 0.84 | 17 | GOL |
| 4 | 102 | 0.45 | 0.79 | 20 | empty |
| 5 | 113 | 0.44 | 0.78 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1465 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1417 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 826 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 826 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 592 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 Q9TQH5
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 2GIT · PDBe 2GIT · UniProt Q9TQH5 · UniProt P61769
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