MolNFT v1 · #126870 · protein

PA3825-eal mn-pgpg structure

5MFU · Diguanylate phosphodiesterase: “PA3825-eal mn-pgpg structure”. X-ray diffraction, 3 ligands (G, MN, NA), 2 pockets (best druggability 0.67). MolNFT v1 #126870 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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.

Pocket	Volume (Å³)	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

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.