Research workbench
Porcine (sus scrofa) major histocompatibility complex, class I, presenting efedltfla
Analyse Porcine (sus scrofa) major histocompatibility complex, class I, presenting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NPZ
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Glu-phe-glu-asp-leu-thr-phe-leu-ala
- UniProt
- B1PJV3, Q07717
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 277 | 28% helix, 40% strand | B1PJV3 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | Q07717 |
| C | Glu-phe-glu-asp-leu-thr-phe-leu-ala | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 684 | 0.70 | 0.78 | 60 | empty |
| 2 | 150 | 0.46 | 0.76 | 25 | PEG, EDO |
| 3 | 73 | 0.41 | 0.80 | 15 | empty |
| 4 | 87 | 0.41 | 0.78 | 22 | EDO |
| 5 | 56 | 0.29 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1348 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 881 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5NPZ · Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting EFEDLTFLA · the same entry in another collection · chain A against A, TM-score 1.00
- Q07717 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q07717) · 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 B1PJV3
- Every structure of UniProt Q07717
- Elsewhere: RCSB PDB 5NPZ · PDBe 5NPZ · UniProt B1PJV3 · UniProt Q07717
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