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Crystal structure of the azotobacter vinelandii bacterioferritin at 2.6 a resolution
Analyse Crystal structure of the azotobacter vinelandii bacterioferritin at 2.6 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SOF
- Type
- protein
- Length
- 1,240 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- UniProt
- P22759
- Ligands
- HEM, FE2, MG, BA
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Bacterioferritin | protein | 155 | 81% helix, 0% strand | P22759 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- FE2 · Fe (II) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, E, D, F, G
- BA · Barium ion · metal · 2 copies · chains A, F, G, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.73 | 0.87 | 33 | HEM |
| 2 | 235 | 0.72 | 0.87 | 33 | HEM |
| 3 | 274 | 0.72 | 0.85 | 32 | HEM |
| 4 | 227 | 0.72 | 0.87 | 32 | HEM |
| 5 | 334 | 0.56 | 0.75 | 37 | empty |
Interfaces
13 interfaces between chains.
- C–D · 911 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 886 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 881 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 540 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1SOF · Crystal structure of the azotobacter vinelandii bacterioferritin at 2.6 A resolution · the same entry in another collection · chain H against H, TM-score 1.00
- P22759 · AlphaFold monomer V2.0 prediction for bacterioferritin (P22759) · a predicted model of the same protein · chain E 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 P22759
- Elsewhere: RCSB PDB 1SOF · PDBe 1SOF · UniProt P22759
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