MolNFT v1 · #125868 · protein
Bacteriophytochrome activated diguanylyl cyclase from idiomarina species A28L
5LLW · Diguanylate cyclase (ggdef) domain-containing protein: “Bacteriophytochrome activated diguanylyl cyclase from idiomarina species A28L”. X-ray diffraction, 2 ligands (LBV, CL), 14 pockets (best druggability 0.84). MolNFT v1 #125868…
- PDB
- 5LLW
- Type
- protein
- Length
- 1,345 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase (ggdef) domain-containing protein
- UniProt
- F7RW09
- Ligands
- LBV, CL
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Diguanylate cyclase (ggdef) domain-containing protein | protein | 673 | 41% helix, 24% strand | F7RW09 |
| A | Diguanylate cyclase (ggdef) domain-containing protein | protein | 672 | 42% helix, 24% strand | F7RW09 |
Ligands and binding sites
- LBV · 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.84 | 0.91 | 59 | LBV |
| 2 | 456 | 0.83 | 0.90 | 55 | LBV |
| 3 | 1172 | 0.78 | 0.80 | 74 | empty |
| 4 | 70 | 0.73 | 0.97 | 16 | empty |
| 5 | 434 | 0.67 | 0.79 | 52 | CL |
Interfaces
1 interface between chains.
- B–A · 3792 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 2 cofactor (engineered, biliverdin attachment).
Compared structures
- 5LLW · Bacteriophytochrome activated diguanylyl cyclase from Idiomarina species A28L · the same entry in another collection · chain B against B, 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 F7RW09
- Elsewhere: RCSB PDB 5LLW · PDBe 5LLW · UniProt F7RW09
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