MolNFT v1 · #163707 · protein
Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from idiomarina species A28L (pr-state monomer).
6SAX · Diguanylate cyclase (ggdef) domain-containing protein: “Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from idiomarina species A28L…”. X-ray diffraction, 1 ligand (LBV), 6 pockets (best druggability…
- PDB
- 6SAX
- Type
- protein
- Length
- 612 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
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Diguanylate cyclase (ggdef) domain-containing protein | protein | 307 | 33% helix, 26% strand | F7RW09 |
| A | Diguanylate cyclase (ggdef) domain-containing protein | protein | 305 | 34% helix, 26% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.87 | 0.88 | 112 | LBV |
| 2 | 296 | 0.60 | 0.78 | 42 | empty |
| 3 | 172 | 0.55 | 0.80 | 17 | empty |
| 4 | 175 | 0.48 | 0.76 | 30 | empty |
| 5 | 60 | 0.40 | 0.80 | 11 | empty |
Interfaces
1 interface between chains.
- B–A · 776 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 6SAX · Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from… · 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 6SAX · PDBe 6SAX · UniProt F7RW09
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