Research workbench
MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and vesicular stomatitis virus nucleoprotein
Analyse MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and vesicular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VAA
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I H-2KB heavy chain; Beta-2 microglobulin; Vesicular stomatitis virus…
- UniProt
- P01901, P01887, P11212
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I H-2KB heavy chain | protein | 274 | 28% helix, 40% strand | P01901 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| P | Vesicular stomatitis virus nucleoprotein | protein | 8 | 0% helix, 0% strand | P11212 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.60 | 0.81 | 30 | empty |
| 2 | 342 | 0.57 | 0.75 | 37 | empty |
| 3 | 67 | 0.52 | 0.86 | 18 | empty |
| 4 | 104 | 0.45 | 0.79 | 21 | empty |
| 5 | 77 | 0.36 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1393 Ų buried · 26 hydrogen bonds · protein-protein
- A–P · 938 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2VAA · MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and vesicular… · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt P11212
- Elsewhere: RCSB PDB 2VAA · PDBe 2VAA · UniProt P01901 · UniProt P01887 · UniProt P11212
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