MolNFT v1 · #24444 · protein
X-ray structure of dps from mycobacterium smegmatis
1UVH · Starvation-induced DNA protecting protein: “X-ray structure of dps from mycobacterium smegmatis”. X-ray diffraction, 1 ligand (FE), 3 pockets (best druggability 0.56). MolNFT v1 #24444 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1UVH
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Starvation-induced DNA protecting protein
- UniProt
- Q8VP75
- Ligands
- FE
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Starvation-induced DNA protecting protein | protein | 157 | 75% helix, 3% strand | Q8VP75 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.56 | 0.88 | 23 | empty |
| 2 | 102 | 0.45 | 0.79 | 14 | empty |
| 3 | 54 | 0.28 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1360 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1324 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 733 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 482 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1UVH · X-ray structure 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 1UVH · PDBe 1UVH · UniProt Q8VP75
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