Research workbench
PA3825-eal mn-pgpg structure
Analyse PA3825-eal mn-pgpg structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MFU
- Type
- protein
- Length
- 254 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate phosphodiesterase
- UniProt
- A0A140SMD7
- Ligands
- G, MN, NA
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate phosphodiesterase | protein | 254 | 44% helix, 22% strand | A0A140SMD7 |
Ligands and binding sites
- G · Guanosine-5'-monophosphate · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- NA · Sodium ion · metal · 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 | 473 | 0.67 | 0.79 | 40 | NA, G |
| 2 | 66 | 0.62 | 0.91 | 19 | empty |
Compared structures
- 5MFU · PA3825-EAL Mn-pGpG 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 5MFU · PDBe 5MFU · UniProt A0A140SMD7
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