Research workbench
Diguanylate cyclase dgcr (I-site mutant) in native state
Analyse Diguanylate cyclase dgcr (I-site mutant) in native state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZXB
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative GGDEF/RESPONSE regulator receiver domain protein
- UniProt
- B0SUI1
- Ligands
- GH3, MG, SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative GGDEF/RESPONSE regulator receiver domain protein | protein | 293 | 49% helix, 21% strand | B0SUI1 |
Ligands and binding sites
- GH3 · 3'-deoxy-guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.57 | 0.77 | 36 | GH3, MG |
| 2 | 143 | 0.57 | 0.82 | 19 | empty |
| 3 | 296 | 0.54 | 0.75 | 41 | GH3 |
| 4 | 157 | 0.51 | 0.79 | 23 | empty |
| 5 | 66 | 0.37 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1745 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6ZXB · Diguanylate cyclase DgcR (I-site mutant) in native state · 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 B0SUI1
- Elsewhere: RCSB PDB 6ZXB · PDBe 6ZXB · UniProt B0SUI1
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