MolNFT v1 · #151752 · protein
The structure of dps from listeria innocua soaked with cobalt
6HX2 · DNA protection during starvation protein: “The structure of dps from listeria innocua soaked with cobalt”. X-ray diffraction, 1 ligand (CO), 14 pockets (best druggability 0.59). MolNFT v1 #151752 on GenesisL1: 3D structure, binding…
- PDB
- 6HX2
- Type
- protein
- Length
- 913 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
- CO
- Pockets
- 14 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | DNA protection during starvation protein (EC 1.16.-.-) | protein | 150 | 75% helix, 0% strand | P80725 |
| B, D | DNA protection during starvation protein (EC 1.16.-.-) | protein | 156 | 74% helix, 0% strand | P80725 |
| F | DNA protection during starvation protein (EC 1.16.-.-) | protein | 151 | 76% helix, 0% strand | P80725 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 45 copies · chains A, D, B, F, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.59 | 0.76 | 48 | CO |
| 2 | 179 | 0.56 | 0.81 | 25 | CO |
| 3 | 122 | 0.43 | 0.77 | 18 | empty |
| 4 | 98 | 0.41 | 0.77 | 18 | empty |
| 5 | 93 | 0.41 | 0.78 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1268 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 1249 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 526 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 519 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6HX2 · The structure of Dps from Listeria innocua soaked with Cobalt · 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 E 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 6HX2 · PDBe 6HX2 · UniProt P80725
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