Research workbench
Structural studies of N terminal deletion mutant of dps from mycobacterium smegmatis
Analyse Structural studies of N terminal deletion mutant of dps from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YW6
- Type
- protein
- Length
- 448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- Q8VP75
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA protection during starvation protein (EC 1.16.-.-) | protein | 148 | 77% helix, 3% strand | Q8VP75 |
| B, C | DNA protection during starvation protein (EC 1.16.-.-) | protein | 150 | 77% helix, 3% strand | Q8VP75 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.66 | 0.78 | 47 | empty |
| 2 | 137 | 0.61 | 0.85 | 15 | empty |
| 3 | 84 | 0.45 | 0.80 | 17 | empty |
| 4 | 170 | 0.45 | 0.75 | 26 | empty |
| 5 | 144 | 0.41 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 446 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 445 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 444 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2YW6 · Structural studies of N terminal deletion mutant of Dps from Mycobacterium smegmatis · 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 Q8VP75
- Elsewhere: RCSB PDB 2YW6 · PDBe 2YW6 · UniProt Q8VP75
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