Research workbench
MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and sendai virus nucleoprotein
Analyse MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and sendai… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VAB
- Type
- protein
- Length
- 382 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; Sendai virus nucleoprotein
- UniProt
- P01901, P01887, P04857
- Pockets
- 6 · best druggability 0.61
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, 39% strand | P01901 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| P | Sendai virus nucleoprotein | protein | 9 | 0% helix, 0% strand | P04857 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.61 | 0.81 | 26 | empty |
| 2 | 379 | 0.58 | 0.76 | 39 | empty |
| 3 | 70 | 0.51 | 0.85 | 18 | empty |
| 4 | 120 | 0.48 | 0.80 | 22 | empty |
| 5 | 62 | 0.41 | 0.80 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1371 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 827 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2VAB · MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and sendai virus… · 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 P04857
- Elsewhere: RCSB PDB 2VAB · PDBe 2VAB · UniProt P01901 · UniProt P01887 · UniProt P04857
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