Research workbench
MHC class I in complex with modified sendai virus nucleoprotein peptide fapgnwpal
Analyse MHC class I in complex with modified 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
- 4PGB
- Type
- protein
- Length
- 772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; Sendai…
- UniProt
- P01901, P01887
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 27% helix, 38% strand | P01901 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Sendai virus nucleoprotein | protein | 9 | 0% helix, 0% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.69 | 0.75 | 71 | empty |
| 2 | 594 | 0.64 | 0.75 | 49 | empty |
| 3 | 298 | 0.56 | 0.76 | 41 | empty |
| 4 | 176 | 0.48 | 0.76 | 30 | empty |
| 5 | 103 | 0.46 | 0.79 | 22 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1223 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1215 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 845 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 844 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 629 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4PGB · MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGNWPAL · the same entry in another collection · chain B against B, 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 0.99
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
- Elsewhere: RCSB PDB 4PGB · PDBe 4PGB · UniProt P01901 · UniProt P01887
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