MolNFT v1 · #52784 · protein
Activated diguanylate cyclase pled in complex with C-di-gmp
2WB4: “Activated diguanylate cyclase pled in complex with C-di-gmp”. X-ray diffraction, 4 ligands (C2E, BEF, MG), 14 pockets (best druggability 0.83). MolNFT v1 #52784 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WB4
- Type
- protein
- Length
- 899 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase
- EC
- 2.7.7.65, 4.6.1.-
- UniProt
- Q9A5I5
- Ligands
- C2E, BEF, MG, SO4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate cyclase (EC 2.7.7.65, 4.6.1.-) | protein | 458 | 48% helix, 19% strand | Q9A5I5 |
| B | Diguanylate cyclase (EC 2.7.7.65, 4.6.1.-) | protein | 441 | 50% helix, 18% strand | Q9A5I5 |
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
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.83 | 0.84 | 126 | SO4 |
| 2 | 271 | 0.70 | 0.85 | 36 | empty |
| 3 | 504 | 0.70 | 0.80 | 54 | empty |
| 4 | 271 | 0.61 | 0.80 | 42 | empty |
| 5 | 274 | 0.58 | 0.78 | 35 | C2E |
Interfaces
1 interface between chains.
- A–B · 3141 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
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 Q9A5I5
- Elsewhere: RCSB PDB 2WB4 · PDBe 2WB4 · UniProt Q9A5I5
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