MolNFT v1 · #103424 · protein
MHC class I in complex with modified sendai virus nucleoprotein peptide fapgnypaf
4PGD · H-2 class I histocompatibility antigen, K-B alpha chain: “MHC class I in complex with modified sendai virus nucleoprotein peptide fapgnypaf”. X-ray diffraction, 7 pockets (best druggability 0.59). MolNFT v1 #103424 on GenesisL1: 3D…
- PDB
- 4PGD
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- 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
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 274 | 26% helix, 39% strand | P01901 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 55% strand | P01887 |
| C | Sendai virus nucleoprotein | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.59 | 0.80 | 27 | empty |
| 2 | 319 | 0.57 | 0.76 | 27 | empty |
| 3 | 165 | 0.55 | 0.80 | 33 | GOL |
| 4 | 128 | 0.47 | 0.79 | 22 | empty |
| 5 | 90 | 0.44 | 0.79 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1406 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 864 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4PGD · MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGNYPAF · 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
- Elsewhere: RCSB PDB 4PGD · PDBe 4PGD · UniProt P01901 · UniProt P01887
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