MolNFT v1 · #65400 · protein
Crystal structure of bacterioferritin from R.SPHAEROIDES
3GVY: “Crystal structure of bacterioferritin from R.SPHAEROIDES”. X-ray diffraction, 2 ligands (HEM, FE), 6 pockets (best druggability 0.74). MolNFT v1 #65400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GVY
- Type
- protein
- Length
- 473 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- UniProt
- Q3J696
- Ligands
- HEM, FE
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacterioferritin | protein | 157 | 75% helix, 0% strand | Q3J696 |
| B, C | Bacterioferritin | protein | 158 | 77% helix, 0% strand | Q3J696 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C, B
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.74 | 0.87 | 31 | HEM |
| 2 | 265 | 0.54 | 0.76 | 34 | empty |
| 3 | 63 | 0.48 | 0.84 | 19 | empty |
| 4 | 65 | 0.42 | 0.81 | 17 | empty |
| 5 | 51 | 0.38 | 0.81 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1041 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 615 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 553 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (heme attachment).
Compared structures
- 3GVY · Crystal structure of bacterioferritin from R.sphaeroides · 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 Q3J696
- Elsewhere: RCSB PDB 3GVY · PDBe 3GVY · UniProt Q3J696
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.