Research workbench
Porcine (sus scrofa) major histocompatibility complex, class I, presenting dferegysl
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
- 5NQ0
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Asp-phe-glu-arg-glu-gly-tyr-ser-leu
- UniProt
- B1PJV3, Q07717
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 28% helix, 41% strand | B1PJV3 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | Q07717 |
| C | Asp-phe-glu-arg-glu-gly-tyr-ser-leu | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.70 | 0.78 | 58 | empty |
| 2 | 133 | 0.44 | 0.76 | 25 | SO4, EDO |
| 3 | 62 | 0.44 | 0.82 | 15 | empty |
| 4 | 82 | 0.42 | 0.79 | 22 | GOL, EDO |
Interfaces
2 interfaces between chains.
- A–B · 1349 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 963 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5NQ0 · Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting DFEREGYSL · 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 5NQ0 · PDBe 5NQ0 · UniProt B1PJV3 · UniProt Q07717
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