Research workbench
Crystal structure of putative diguanylate CYCLASE/PHOSPHODIESTERASE complex with cyclic di-gmp
Analyse Crystal structure of putative diguanylate CYCLASE/PHOSPHODIESTERASE complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N3T
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative diguanylate CYCLASE/PHOSPHODIESTERASE
- UniProt
- Q3SJE6
- Ligands
- C2E, MG, CL
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative diguanylate CYCLASE/PHOSPHODIESTERASE | protein | 260 | 51% helix, 23% strand | Q3SJE6 |
| B | Putative diguanylate CYCLASE/PHOSPHODIESTERASE | protein | 261 | 52% helix, 22% strand | Q3SJE6 |
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
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.58 | 0.78 | 36 | C2E |
| 2 | 288 | 0.58 | 0.77 | 37 | C2E |
| 3 | 100 | 0.57 | 0.85 | 21 | empty |
| 4 | 92 | 0.56 | 0.86 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3N3T · Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic… · 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 Q3SJE6
- Elsewhere: RCSB PDB 3N3T · PDBe 3N3T · UniProt Q3SJE6
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