Research workbench
Mycobacterium smegmatis dps hexagonal form
Analyse Mycobacterium smegmatis dps hexagonal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VEQ
- Type
- protein
- Length
- 1,896 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Starvation-induced DNA protecting protein
- UniProt
- Q8VP75
- Ligands
- FE
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Starvation-induced DNA protecting protein | protein | 158 | 73% helix, 3% strand | Q8VP75 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, J, B, E, C, I, D, G, F, L, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.67 | 0.94 | 15 | empty |
| 2 | 68 | 0.66 | 0.93 | 15 | empty |
| 3 | 69 | 0.66 | 0.93 | 16 | empty |
| 4 | 61 | 0.64 | 0.93 | 15 | empty |
| 5 | 369 | 0.63 | 0.78 | 42 | empty |
Interfaces
30 interfaces between chains.
- C–I · 1575 Ų buried · 30 hydrogen bonds · protein-protein
- H–K · 1573 Ų buried · 30 hydrogen bonds · protein-protein
- B–E · 1570 Ų buried · 30 hydrogen bonds · protein-protein
- A–J · 1570 Ų buried · 30 hydrogen bonds · protein-protein
- D–G · 1560 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1VEQ · Mycobacterium smegmatis Dps Hexagonal 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 1VEQ · PDBe 1VEQ · UniProt Q8VP75
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