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PA3825-eal mg-cdg structure

Analyse PA3825-eal mg-cdg structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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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