Research workbench
Crystal structure of E. COLI bacterioferritin (bfr) with two ZN(II) ion sites at the ferroxidase centre (zn-bfr).
Analyse Crystal structure of E. COLI bacterioferritin (bfr) with two ZN(II) ion sites… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E1O
- Type
- protein
- Length
- 1,872 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- UniProt
- P0ABD3
- Ligands
- HEM, ZN, SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Bacterioferritin | protein | 156 | 79% helix, 0% strand | P0ABD3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 16 copies · chains A, J, B, C, H, D, E, F, I, K, G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.72 | 0.87 | 35 | HEM |
| 2 | 217 | 0.72 | 0.87 | 32 | HEM |
| 3 | 236 | 0.72 | 0.87 | 32 | HEM |
| 4 | 213 | 0.71 | 0.87 | 31 | HEM |
| 5 | 224 | 0.71 | 0.86 | 32 | HEM |
Interfaces
24 interfaces between chains.
- A–B · 942 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 941 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 940 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 938 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 937 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3E1O · Crystal structure of E. coli Bacterioferritin (BFR) with two ZN(II) ION sites at the… · the same entry in another collection · chain L against L, 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 P0ABD3
- Elsewhere: RCSB PDB 3E1O · PDBe 3E1O · UniProt P0ABD3
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