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Bacteriophytochrome activated diguanylyl cyclase from idiomarina species A28L with GTP bound
Analyse Bacteriophytochrome activated diguanylyl cyclase from idiomarina species A28L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LLX
- Type
- protein
- Length
- 1,321 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase (ggdef) domain-containing protein
- EC
- 2.7.7.65
- UniProt
- F7RW09
- Ligands
- LBV, GTP, MG, CL
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate cyclase (ggdef) domain-containing protein (EC 2.7.7.65) | protein | 667 | 42% helix, 24% strand | F7RW09 |
| B | Diguanylate cyclase (ggdef) domain-containing protein (EC 2.7.7.65) | protein | 654 | 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 A, B
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.85 | 0.93 | 52 | LBV |
| 2 | 437 | 0.83 | 0.90 | 57 | LBV |
| 3 | 1079 | 0.81 | 0.83 | 78 | GTP, MG |
| 4 | 71 | 0.72 | 0.96 | 15 | empty |
| 5 | 457 | 0.67 | 0.79 | 51 | CL |
Interfaces
1 interface between chains.
- A–B · 4076 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 5LLX · Bacteriophytochrome activated diguanylyl cyclase from Idiomarina species A28L with GTP… · 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 5LLX · PDBe 5LLX · UniProt F7RW09
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