Research workbench
Mycobacterium smegmatis dps tetragonal form
Analyse Mycobacterium smegmatis dps tetragonal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VEL
- Type
- protein
- Length
- 983 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Starvation-induced DNA protecting protein
- UniProt
- Q8VP75
- Ligands
- CD, NA, SO4
- Pockets
- 17 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F | Starvation-induced DNA protecting protein | protein | 163 | 71% helix, 2% strand | Q8VP75 |
| C | Starvation-induced DNA protecting protein | protein | 166 | 69% helix, 5% strand | Q8VP75 |
| E | Starvation-induced DNA protecting protein | protein | 165 | 70% helix, 4% strand | Q8VP75 |
Ligands and binding sites
- CD · Cadmium ion · metal · 10 copies · chains A, B, C, E, D, F
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.65 | 0.77 | 46 | empty |
| 2 | 466 | 0.65 | 0.78 | 47 | empty |
| 3 | 61 | 0.62 | 0.92 | 15 | NA, SO4 |
| 4 | 76 | 0.59 | 0.89 | 16 | NA, SO4 |
| 5 | 92 | 0.43 | 0.79 | 17 | empty |
Interfaces
9 interfaces between chains.
- C–E · 1421 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 791 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 789 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 789 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 770 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1VEL · Mycobacterium smegmatis Dps tetragonal form · 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 1VEL · PDBe 1VEL · UniProt Q8VP75
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