Research workbench
Crystal structure of the coiled coil and ggdef domain of dgcb from caulobacter crescentus in complex with C-di-gmp
Analyse Crystal structure of the coiled coil and ggdef domain of dgcb from caulobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TTR
- Type
- protein
- Length
- 386 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ggdef diguanylate cyclase dgcb
- UniProt
- A0A0H3CAN8
- Ligands
- C2E, PO4
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ggdef diguanylate cyclase dgcb | protein | 191 | 53% helix, 17% strand | A0A0H3CAN8 |
| B | Ggdef diguanylate cyclase dgcb | protein | 195 | 54% helix, 18% 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 · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.73 | 0.77 | 89 | PO4, C2E |
Interfaces
1 interface between chains.
- A–B · 1222 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6TTR · Crystal Structure of the coiled coil and GGDEF domain of DgcB from Caulobacter crescentus… · 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 6TTR · PDBe 6TTR · UniProt A0A0H3CAN8
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