MolNFT v2 · #225561 · protein
ASFV p72 in complex with Fab B1
8Y3O · B646L: “ASFV p72 in complex with Fab B1”. Electron microscopy at 2.75, 20 pockets (best druggability 0.83). MolNFT v2 #225561 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8Y3O
- Type
- protein
- Length
- 2,163 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- African swine fever virus; Sus scrofa
- Molecule
- B646L; Light chain of B1; Heavy chain of B1
- UniProt
- Q5IZK2
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 2.75 · 3 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | B646L | protein | 487 | 10% helix, 40% strand | Q5IZK2 |
| D, E, F | Light chain of B1 | protein | 111 | 0% helix, 40% strand | — |
| H, G, I | Heavy chain of B1 | protein | 123 | 5% helix, 47% strand | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.83 | 0.85 | 85 | empty |
| 2 | 708 | 0.83 | 0.87 | 81 | empty |
| 3 | 806 | 0.82 | 0.85 | 93 | empty |
| 4 | 516 | 0.80 | 0.87 | 57 | empty |
| 5 | 727 | 0.79 | 0.83 | 99 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3112 Ų buried · 29 hydrogen bonds · protein-protein
- C–B · 3091 Ų buried · 27 hydrogen bonds · protein-protein
- C–A · 3076 Ų buried · 31 hydrogen bonds · protein-protein
- E–G · 832 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 831 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
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 Q5IZK2
- Elsewhere: RCSB PDB 8Y3O · PDBe 8Y3O · UniProt Q5IZK2
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