MolNFT v1 · #86501 · protein
Cytochrome B5 of ostreococcus tauri virus 2
4B8N · Cytochrome B5-host origin: “Cytochrome B5 of ostreococcus tauri virus 2”. X-ray diffraction, 2 ligands (HEM, SO4), 6 pockets (best druggability 0.67). MolNFT v1 #86501 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4B8N
- Type
- protein
- Length
- 333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B5-host origin
- UniProt
- E4WM77
- Ligands
- HEM, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B5-host origin | protein | 79 | 35% helix, 24% strand | E4WM77 |
| B | Cytochrome B5-host origin | protein | 90 | 38% helix, 19% strand | E4WM77 |
| C | Cytochrome B5-host origin | protein | 81 | 40% helix, 21% strand | E4WM77 |
| D | Cytochrome B5-host origin | protein | 83 | 37% helix, 22% strand | E4WM77 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.67 | 0.86 | 23 | HEM |
| 2 | 209 | 0.66 | 0.84 | 27 | HEM |
| 3 | 138 | 0.64 | 0.86 | 19 | HEM |
| 4 | 130 | 0.63 | 0.85 | 20 | HEM |
| 5 | 50 | 0.60 | 0.92 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 612 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 406 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4B8N · Cytochrome b5 of Ostreococcus tauri virus 2 · the same entry in another collection · chain A against A, TM-score 1.00
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 E4WM77
- Elsewhere: RCSB PDB 4B8N · PDBe 4B8N · UniProt E4WM77
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