MolNFT v1 · #34115 · protein
Crystal structure of dps from staphylococcus aureus
2D5K · Dps family protein: “Crystal structure of dps from staphylococcus aureus”. X-ray diffraction, 3 pockets (best druggability 0.32). MolNFT v1 #34115 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2D5K
- Type
- protein
- Length
- 591 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dps family protein
- EC
- 4.2.1.52
- UniProt
- Q5HE61
- Pockets
- 3 · best druggability 0.32
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dps family protein (EC 4.2.1.52) | protein | 148 | 79% helix, 0% strand | Q5HE61 |
| B | Dps family protein (EC 4.2.1.52) | protein | 149 | 79% helix, 0% strand | Q5HE61 |
| C, D | Dps family protein (EC 4.2.1.52) | protein | 147 | 80% helix, 0% strand | Q5HE61 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.32 | 0.77 | 11 | empty |
| 2 | 80 | 0.31 | 0.74 | 23 | empty |
| 3 | 57 | 0.31 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1209 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1187 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 492 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 434 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2D5K · Crystal structure of Dps from Staphylococcus aureus · 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 Q5HE61
- Elsewhere: RCSB PDB 2D5K · PDBe 2D5K · UniProt Q5HE61
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