Research workbench
Ggdef domain of dcsbis complexed with C-di-gmp
Analyse Ggdef domain of dcsbis complexed with C-di-gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZMM
- Type
- protein
- Length
- 325 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase
- EC
- 2.7.7.65
- UniProt
- Q9I072
- Ligands
- C2E
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate cyclase (EC 2.7.7.65) | protein | 164 | 46% helix, 25% strand | Q9I072 |
| B | Diguanylate cyclase (EC 2.7.7.65) | protein | 161 | 48% helix, 24% strand | Q9I072 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.53 | 0.74 | 35 | C2E |
| 2 | 61 | 0.43 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 118 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZMM · GGDEF domain of Dcsbis complexed with c-di-GMP · 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 Q9I072
- Elsewhere: RCSB PDB 4ZMM · PDBe 4ZMM · UniProt Q9I072
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