Research workbench
Crystal structure of B*4402 presenting a 10MER EBV epitope
Analyse Crystal structure of B*4402 presenting a 10MER EBV epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DX6
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility complex HLA-B*4402; Beta-2-microglobulin; EBV decapeptide…
- UniProt
- P30481, P61769, P03204
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility complex HLA-B*4402 | protein | 276 | 28% helix, 40% strand | P30481 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | EBV decapeptide epitope | protein | 10 | 0% helix, 0% strand | P03204 |
Ligands and binding sites
- ACT · Acetate ion · additive · 9 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.70 | 0.78 | 55 | ACT |
| 2 | 149 | 0.50 | 0.79 | 26 | ACT |
| 3 | 101 | 0.45 | 0.79 | 23 | GOL |
| 4 | 57 | 0.36 | 0.79 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1327 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 948 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 P30481
- Every structure of UniProt P61769
- Every structure of UniProt P03204
- Elsewhere: RCSB PDB 3DX6 · PDBe 3DX6 · UniProt P30481 · UniProt P61769 · UniProt P03204
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