MolNFT v1 · #50042 · protein
Crystal structure of putative diguanylate CYCLASE/PHOSPHODIESTERASE from thiobacillus denitrificans
2R6O · Putative diguanylate CYCLASE/PHOSPHODIESTERASE (ggdef & eal…: “Crystal structure of putative diguanylate CYCLASE/PHOSPHODIESTERASE from thiobacillus denitrificans”. X-ray diffraction, 2 ligands (MG, CL), 4 pockets (best druggability…
- PDB
- 2R6O
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative diguanylate CYCLASE/PHOSPHODIESTERASE (ggdef & eal domains)
- UniProt
- Q3SJE6
- Ligands
- MG, CL
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative diguanylate CYCLASE/PHOSPHODIESTERASE (ggdef & eal domains) | protein | 258 | 50% helix, 22% strand | Q3SJE6 |
| B | Putative diguanylate CYCLASE/PHOSPHODIESTERASE (ggdef & eal domains) | protein | 242 | 50% helix, 21% strand | Q3SJE6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.59 | 0.87 | 21 | empty |
| 2 | 312 | 0.58 | 0.77 | 37 | CL |
| 3 | 85 | 0.55 | 0.86 | 22 | empty |
| 4 | 109 | 0.38 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2R6O · Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus… · 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 Q3SJE6
- Elsewhere: RCSB PDB 2R6O · PDBe 2R6O · UniProt Q3SJE6
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