Research workbench
Achromobacter DH1F bacterioferritin
Analyse Achromobacter DH1F bacterioferritin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZUR
- Type
- protein
- Length
- 463 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- Ligands
- HEM, FE2, BA, CL
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bacterioferritin | protein | 154 | 81% helix, 0% strand | — |
| B | Bacterioferritin | protein | 155 | 81% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- BA · Barium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.42 | 0.78 | 17 | PEG |
| 2 | 95 | 0.40 | 0.77 | 18 | PEG |
| 3 | 88 | 0.39 | 0.77 | 16 | PEG |
| 4 | 62 | 0.29 | 0.74 | 13 | empty |
| 5 | 65 | 0.28 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 573 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5ZUR · Achromobacter Dh1f Bacterioferritin · 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
- Elsewhere: RCSB PDB 5ZUR · PDBe 5ZUR
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