MolNFT v1 · #139860 · protein
The catalytic domain of gdpp
5XSI · Phosphodiesterase acting on cyclic dinucleotides: “The catalytic domain of gdpp”. X-ray diffraction, 1 ligand (MN), 2 pockets (best druggability 0.76). MolNFT v1 #139860 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XSI
- 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
- MN
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphodiesterase acting on cyclic dinucleotides | protein | 333 | 46% helix, 20% strand | A0A0U1MUE2 |
Ligands and binding sites
- 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 | 1044 | 0.76 | 0.79 | 55 | empty |
| 2 | 51 | 0.28 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1698 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5XSI · The catalytic domain of GdpP · 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 5XSI · PDBe 5XSI · UniProt A0A0U1MUE2
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