MolNFT v1 · #126845 · protein
PA3825-eal mg-cdg structure
5MF5 · Diguanylate phosphodiesterase: “PA3825-eal mg-cdg structure”. X-ray diffraction, 2 ligands (C2E, MG), 2 pockets (best druggability 0.68). MolNFT v1 #126845 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MF5
- Type
- protein
- Length
- 256 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate phosphodiesterase
- UniProt
- A0A140SMD7
- Ligands
- C2E, MG
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate phosphodiesterase | protein | 256 | 47% helix, 21% strand | A0A140SMD7 |
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 · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.68 | 0.80 | 40 | C2E, MG |
| 2 | 55 | 0.58 | 0.91 | 19 | empty |
Compared structures
- 5MF5 · PA3825-EAL Mg-CdG Structure · 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 A0A140SMD7
- Elsewhere: RCSB PDB 5MF5 · PDBe 5MF5 · UniProt A0A140SMD7
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