Research workbench
HLA-A2.1 kvaeivhfl
Analyse HLA-A2.1 kvaeivhfl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V5H
- 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; HIV-based…
- UniProt
- P01892, P61769
- Pockets
- 6 · best druggability 0.77
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, 40% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | HIV-based altered-peptide ligand kvaeivhfl | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.77 | 0.79 | 101 | empty |
| 2 | 636 | 0.70 | 0.78 | 52 | empty |
| 3 | 122 | 0.47 | 0.79 | 25 | empty |
| 4 | 83 | 0.37 | 0.76 | 16 | empty |
| 5 | 53 | 0.33 | 0.78 | 16 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1466 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1436 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 907 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 892 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 278 Ų buried · 2 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3V5H · PDBe 3V5H · UniProt P01892 · UniProt P61769
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