Research workbench
Structure of dps from listeria innocua soaked with 10 mm zinc for 120 minutes
Analyse Structure of dps from listeria innocua soaked with 10 mm zinc for 120 minutes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SEV
- Type
- protein
- Length
- 896 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA STARVATION/STATIONARY phase protection protein
- UniProt
- A0A3T1N4C4
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | DNA STARVATION/STATIONARY phase protection protein | protein | 150 | 75% helix, 0% strand | A0A3T1N4C4 |
| C | DNA STARVATION/STATIONARY phase protection protein | protein | 146 | 77% helix, 0% strand | A0A3T1N4C4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 21 copies · chains A, D, B, F, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.61 | 0.76 | 54 | ZN |
| 2 | 149 | 0.55 | 0.81 | 27 | ZN |
| 3 | 248 | 0.53 | 0.76 | 31 | empty |
| 4 | 116 | 0.49 | 0.81 | 20 | ZN |
| 5 | 142 | 0.45 | 0.76 | 19 | empty |
Interfaces
10 interfaces between chains.
- B–E · 1293 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1286 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 536 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 526 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 523 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6SEV · Structure of Dps from Listeria innocua soaked with 10 mM zinc for 120 minutes · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A3T1N4C4
- Elsewhere: RCSB PDB 6SEV · PDBe 6SEV · UniProt A0A3T1N4C4
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