MolNFT v1 · #32899 · protein
X-ray structure of dps from thermosynechococcus elongatus
2C41 · Dps family DNA-binding stress response protein: “X-ray structure of dps from thermosynechococcus elongatus”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.65). MolNFT v1 #32899 on GenesisL1: 3D structure, binding…
- PDB
- 2C41
- Type
- protein
- Length
- 1,853 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dps family DNA-binding stress response protein
- UniProt
- Q8DG54
- Ligands
- CL
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Dps family DNA-binding stress response protein | protein | 155 | 75% helix, 0% strand | Q8DG54 |
| B, D, E, G, H, I | Dps family DNA-binding stress response protein | protein | 154 | 76% helix, 0% strand | Q8DG54 |
| C | Dps family DNA-binding stress response protein | protein | 157 | 75% helix, 0% strand | Q8DG54 |
| F | Dps family DNA-binding stress response protein | protein | 156 | 76% helix, 0% strand | Q8DG54 |
| J, K | Dps family DNA-binding stress response protein | protein | 153 | 76% helix, 0% strand | Q8DG54 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, D, F, B, I, L, C, G, K, E, H, J
- PGE · Triethylene glycol · additive · 12 copies · chains B, D, L, C, F, E, I, A, H, G
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, D, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.65 | 0.80 | 31 | empty |
| 2 | 363 | 0.65 | 0.79 | 32 | empty |
| 3 | 328 | 0.64 | 0.80 | 32 | empty |
| 4 | 336 | 0.63 | 0.79 | 29 | empty |
| 5 | 570 | 0.63 | 0.75 | 70 | PGE |
Interfaces
30 interfaces between chains.
- I–J · 1238 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1238 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1236 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1231 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1224 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2C41 · X-ray structure of Dps from Thermosynechococcus elongatus · the same entry in another collection · chain I against I, 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 Q8DG54
- Elsewhere: RCSB PDB 2C41 · PDBe 2C41 · UniProt Q8DG54
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