MolNFT v1 · #125870 · protein
Photosensory module of bacteriophytochrome linked diguanylyl cyclase from idiomarina species A28L
5LLY · Diguanylate cyclase (ggdef) domain-containing protein: “Photosensory module of bacteriophytochrome linked diguanylyl cyclase from idiomarina species A28L”. X-ray diffraction, 2 ligands (LBV, CL), 20 pockets (best druggability 0.84).…
- PDB
- 5LLY
- Type
- protein
- Length
- 2,013 residues
- Chains
- 4
- 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
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Diguanylate cyclase (ggdef) domain-containing protein | protein | 502 | 37% helix, 25% strand | F7RW09 |
| A | Diguanylate cyclase (ggdef) domain-containing protein | protein | 512 | 39% helix, 27% strand | F7RW09 |
| C | Diguanylate cyclase (ggdef) domain-containing protein | protein | 509 | 39% helix, 26% strand | F7RW09 |
| B | Diguanylate cyclase (ggdef) domain-containing protein | protein | 490 | 38% 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 · 4 copies · chains D, A, C, B
- CL · Chloride ion · ion · 8 copies · chains D, A, C, B
- GOL · Glycerol · additive · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.84 | 0.91 | 56 | LBV |
| 2 | 434 | 0.84 | 0.91 | 60 | LBV |
| 3 | 378 | 0.83 | 0.92 | 56 | LBV |
| 4 | 458 | 0.83 | 0.90 | 61 | LBV |
| 5 | 1029 | 0.83 | 0.84 | 78 | CL |
Interfaces
5 interfaces between chains.
- D–C · 2855 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2823 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 766 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 252 Ų buried · 3 hydrogen bonds · protein-protein
- D–A · 228 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (biliverdin attachment).
Compared structures
- 5LLY · Photosensory Module of Bacteriophytochrome linked Diguanylyl Cyclase from Idiomarina… · the same entry in another collection · chain D against D, 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 5LLY · PDBe 5LLY · UniProt F7RW09
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