MolNFT v1 · #69648 · protein
Crystal structure of putative bacterioferritin from campylobacter jejuni
3KWO: “Crystal structure of putative bacterioferritin from campylobacter jejuni”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.69). MolNFT v1 #69648 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KWO
- Type
- protein
- Length
- 591 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative bacterioferritin
- UniProt
- Q0P891
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative bacterioferritin | protein | 149 | 76% helix, 1% strand | Q0P891 |
| B, C | Putative bacterioferritin | protein | 147 | 77% helix, 1% strand | Q0P891 |
| D | Putative bacterioferritin | protein | 148 | 78% helix, 1% strand | Q0P891 |
Ligands and binding sites
- ZN · Zinc ion · metal · 26 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 24 copies · chains A, C, B, D
- BU1 · 1,4-butanediol · additive · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 805 | 0.69 | 0.75 | 84 | empty |
| 2 | 230 | 0.58 | 0.79 | 24 | GOL, BU1 |
| 3 | 67 | 0.37 | 0.78 | 13 | ACY, ZN |
| 4 | 61 | 0.36 | 0.78 | 17 | empty |
| 5 | 57 | 0.34 | 0.77 | 14 | ACY, ZN |
Interfaces
5 interfaces between chains.
- A–C · 1234 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 486 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 346 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 329 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3KWO · Crystal Structure of Putative Bacterioferritin from Campylobacter jejuni · the same entry in another collection · chain D against D, TM-score 1.00
- Q0P891 · AlphaFold monomer V2.0 prediction for DNA protection during starvation protein (Q0P891) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q0P891
- Elsewhere: RCSB PDB 3KWO · PDBe 3KWO · UniProt Q0P891
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