MolNFT v1 · #147970 · protein
Activated heterodimer of the bacteriophytochrome regulated diguanylyl cyclase variant - S505V A526V - from idiomarina species A28L
6ET7 · Diguanylate cyclase (ggdef) domain-containing protein: “Activated heterodimer of the bacteriophytochrome regulated diguanylyl cyclase variant - S505V A526V - from…”. X-ray diffraction, 2 ligands (LBV, CL), 15 pockets (best…
- PDB
- 6ET7
- Type
- protein
- Length
- 1,291 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
- 15 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate cyclase (ggdef) domain-containing protein | protein | 646 | 44% helix, 22% strand | F7RW09 |
| B | Diguanylate cyclase (ggdef) domain-containing protein | protein | 645 | 43% helix, 23% 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 A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.83 | 0.90 | 57 | LBV |
| 2 | 423 | 0.82 | 0.90 | 51 | LBV |
| 3 | 551 | 0.76 | 0.83 | 50 | empty |
| 4 | 1067 | 0.75 | 0.78 | 75 | empty |
| 5 | 66 | 0.71 | 0.96 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3110 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 6ET7 · Activated heterodimer of the bacteriophytochrome regulated diguanylyl cyclase variant… · 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 F7RW09
- Elsewhere: RCSB PDB 6ET7 · PDBe 6ET7 · UniProt F7RW09
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