Research workbench
The X-ray crystal structure of the listeria innocua H31G dps mutant.
Analyse The X-ray crystal structure of the listeria innocua H31G dps mutant. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BK6
- Type
- protein
- Length
- 904 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-heme iron-containing ferritin
- UniProt
- P80725
- Pockets
- 12 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Non-heme iron-containing ferritin | protein | 150 | 75% helix, 0% strand | P80725 |
| C | Non-heme iron-containing ferritin | protein | 154 | 73% helix, 0% strand | P80725 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.58 | 0.75 | 51 | empty |
| 2 | 323 | 0.55 | 0.75 | 34 | empty |
| 3 | 156 | 0.51 | 0.79 | 29 | empty |
| 4 | 127 | 0.51 | 0.80 | 26 | empty |
| 5 | 108 | 0.41 | 0.76 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1282 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1266 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 545 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 532 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 529 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2BK6 · The X-ray crystal structure of the Listeria innocua H31G Dps mutant. · the same entry in another collection · chain F against F, TM-score 1.00
- P80725 · AlphaFold monomer V2.0 prediction for DNA protection during starvation protein (P80725) · a predicted model of the same protein · chain F 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 P80725
- Elsewhere: RCSB PDB 2BK6 · PDBe 2BK6 · UniProt P80725
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