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The structure of Dps from Listeria innocua soaked before soaking experiments with Zn, Co and La
Analyse The structure of Dps from Listeria innocua soaked before soaking experiments… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HVQ
- Type
- protein
- Length
- 908 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- P80725
- Ligands
- LA
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · resolution 1.9 · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA protection during starvation protein (EC 1.16.-.-) | protein | 152 | 74% helix, 0% strand | P80725 |
| B, C, D, F | DNA protection during starvation protein (EC 1.16.-.-) | protein | 151 | 75% helix, 0% strand | P80725 |
| E | DNA protection during starvation protein (EC 1.16.-.-) | protein | 152 | 74% helix, 0% strand | P80725 |
Ligands and binding sites
- LA · Lanthanum (III) ion · metal · 50 copies · chains A, C, E, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.59 | 0.76 | 46 | empty |
| 2 | 157 | 0.57 | 0.82 | 30 | empty |
| 3 | 164 | 0.57 | 0.81 | 33 | empty |
| 4 | 288 | 0.52 | 0.74 | 35 | LA |
| 5 | 124 | 0.49 | 0.81 | 19 | LA |
Interfaces
10 interfaces between chains.
- E–F · 1250 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1236 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 541 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 532 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HVQ · The structure of dps from listeria innocua soaked before soaking experiments with zn, co… · 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 C 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 6HVQ · PDBe 6HVQ · UniProt P80725
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