MolNFT v1 · #165391 · protein
Crystal structure of the ggdef domain of dgcb from caulobacter crescentus in complex with C-di-gmp
6TTS · Ggdef diguanylate cyclase dgcb: “Crystal structure of the ggdef domain of dgcb from caulobacter crescentus in complex with C-di-gmp”. X-ray diffraction, 2 ligands (C2E, SO4), 4 pockets (best druggability 0.58). MolNFT v1 #165391 on…
- PDB
- 6TTS
- Type
- protein
- Length
- 347 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ggdef diguanylate cyclase dgcb
- UniProt
- A0A0H3CAN8
- Ligands
- C2E, SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ggdef diguanylate cyclase dgcb | protein | 171 | 43% helix, 19% strand | A0A0H3CAN8 |
| B | Ggdef diguanylate cyclase dgcb | protein | 176 | 43% helix, 20% strand | A0A0H3CAN8 |
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 · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.58 | 0.78 | 34 | C2E |
| 2 | 197 | 0.56 | 0.80 | 39 | C2E, SO4 |
| 3 | 74 | 0.50 | 0.84 | 22 | SO4 |
| 4 | 181 | 0.49 | 0.77 | 28 | C2E |
Interfaces
1 interface between chains.
- A–B · 960 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6TTS · Crystal structure of the GGDEF domain of DgcB from Caulobacter crescentus in complex with… · 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 A0A0H3CAN8
- Elsewhere: RCSB PDB 6TTS · PDBe 6TTS · UniProt A0A0H3CAN8
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