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Crystal structure of Dps1 from the thermophilic non-heterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O-77
Analyse Crystal structure of Dps1 from the thermophilic non-heterocystous filamentous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKP
- Type
- protein
- Length
- 1,001 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Leptolyngbya sp. O-77
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- A0A0X8WZ56
- Ligands
- ZN, FE
- Pockets
- 12 · best druggability 0.55
Structure
x-ray diffraction · resolution 2.9 · 6 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA protection during starvation protein (EC 1.16.-.-) | protein | 171 | 68% helix, 0% strand | A0A0X8WZ56 |
| B | DNA protection during starvation protein (EC 1.16.-.-) | protein | 168 | 70% helix, 1% strand | A0A0X8WZ56 |
| C | DNA protection during starvation protein (EC 1.16.-.-) | protein | 172 | 67% helix, 1% strand | A0A0X8WZ56 |
| D | DNA protection during starvation protein (EC 1.16.-.-) | protein | 170 | 69% helix, 1% strand | A0A0X8WZ56 |
| E | DNA protection during starvation protein (EC 1.16.-.-) | protein | 167 | 71% helix, 1% strand | A0A0X8WZ56 |
| F | DNA protection during starvation protein (EC 1.16.-.-) | protein | 153 | 73% helix, 0% strand | A0A0X8WZ56 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, F, E
- FE · Fe (III) ion · metal · 12 copies · chains A, D, B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.55 | 0.77 | 42 | ZN |
| 2 | 72 | 0.53 | 0.86 | 25 | FE |
| 3 | 68 | 0.46 | 0.83 | 17 | empty |
| 4 | 101 | 0.44 | 0.79 | 17 | FE |
| 5 | 75 | 0.41 | 0.79 | 15 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1728 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1709 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 849 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 837 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 789 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LKP · Crystal structure of DPS1 from the thermophilic non-heterocystous filamentous… · 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 A0A0X8WZ56
- Elsewhere: RCSB PDB 6LKP · PDBe 6LKP · UniProt A0A0X8WZ56
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