MolNFT v1 · #151706 · protein
The structure of dps from listeria innocua soaked before soaking experiments with zn, co and la
6HVQ · DNA protection during starvation protein: “The structure of dps from listeria innocua soaked before soaking experiments with zn, co and la”. X-ray diffraction, 1 ligand (LA), 13 pockets (best druggability 0.59). MolNFT v1 #151706 on…
- PDB
- 6HVQ
- Type
- protein
- Length
- 908 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- P80725
- Ligands
- LA
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · 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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