MolNFT v1 · #64163 · protein
Crystal structure of ferritin (bacterioferritin) from brucella melitensis
3FVB: “Crystal structure of ferritin (bacterioferritin) from brucella melitensis”. X-ray diffraction, 5 ligands (HEM, MG, FE), 2 pockets (best druggability 0.72). MolNFT v1 #64163 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3FVB
- Type
- protein
- Length
- 322 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- UniProt
- Q2YKI4
- Ligands
- HEM, MG, FE, NA, CL
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacterioferritin | protein | 161 | 78% helix, 1% strand | Q2YKI4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- FE · Fe (III) ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.72 | 0.87 | 29 | HEM |
| 2 | 52 | 0.57 | 0.91 | 19 | IMD |
Interfaces
1 interface between chains.
- A–B · 1047 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3FVB · Crystal structure of ferritin (bacterioferritin) from Brucella melitensis · 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 Q2YKI4
- Elsewhere: RCSB PDB 3FVB · PDBe 3FVB · UniProt Q2YKI4
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