Research workbench
The catalytic domain of gdpp with C-di-AMP
Analyse The catalytic domain of gdpp with C-di-AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XSN
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase acting on cyclic dinucleotides
- UniProt
- A0A0U1MUE2
- Ligands
- 2BA, MN
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphodiesterase acting on cyclic dinucleotides | protein | 333 | 45% helix, 19% strand | A0A0U1MUE2 |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 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 | 1086 | 0.75 | 0.78 | 62 | empty |
| 2 | 51 | 0.27 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1641 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5XSN · The catalytic domain of GdpP with c-di-AMP · 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 A0A0U1MUE2
- Elsewhere: RCSB PDB 5XSN · PDBe 5XSN · UniProt A0A0U1MUE2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.