Research workbench
MHC class I H-2DB complexed with a sendai virus nucleoprotein peptide
Analyse MHC class I H-2DB complexed with a sendai virus nucleoprotein peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CE6
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (MHC class I H-2DB heavy chain); Protein (human beta-2 microglobulin); Protein…
- UniProt
- P01899, P61769, P04858
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (MHC class I H-2DB heavy chain) | protein | 274 | 26% helix, 38% strand | P01899 |
| B | Protein (human beta-2 microglobulin) | protein | 99 | 0% helix, 48% strand | P61769 |
| C | Protein (sendai virus nucleoprotein) | protein | 9 | 0% helix, 0% strand | P04858 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.69 | 0.77 | 55 | empty |
| 2 | 88 | 0.47 | 0.81 | 17 | empty |
| 3 | 135 | 0.43 | 0.76 | 31 | empty |
| 4 | 99 | 0.41 | 0.77 | 18 | empty |
| 5 | 51 | 0.26 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1277 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 843 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1CE6 · MHC class I H-2DB complexed with a sendai virus nucleoprotein peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P01899
- Every structure of UniProt P61769
- Every structure of UniProt P04858
- Elsewhere: RCSB PDB 1CE6 · PDBe 1CE6 · UniProt P01899 · UniProt P61769 · UniProt P04858
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