Research workbench
The catalytic domain of gdpp with C-di-gmp
Analyse The catalytic domain of gdpp with C-di-gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XT3
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase acting on cyclic dinucleotides
- UniProt
- A0A0U1MUE2
- Ligands
- C2E, MN
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase acting on cyclic dinucleotides | protein | 332 | 43% helix, 20% strand | A0A0U1MUE2 |
| B | Phosphodiesterase acting on cyclic dinucleotides | protein | 333 | 43% helix, 18% strand | A0A0U1MUE2 |
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
- MN · Manganese (II) ion · metal · 3 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 | 875 | 0.74 | 0.78 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 1678 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5XT3 · The catalytic domain of GdpP with c-di-GMP · 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 5XT3 · PDBe 5XT3 · UniProt A0A0U1MUE2
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