MolNFT v1 · #117113 · protein

Crystal structure of the cgmp-dependent protein kinase pkg from plasmodium falciparum - apo form

5DYK: “Crystal structure of the cgmp-dependent protein kinase pkg from plasmodium falciparum - apo form”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.75). MolNFT v1 #117113 on GenesisL1: 3D structure, binding sites…

PDB: 5DYK
Type: protein
Length: 809 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cgmp-dependent protein kinase
UniProt: Q8MMZ4
Ligands: SO4
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cgmp-dependent protein kinase	protein	809	35% helix, 26% strand	Q8MMZ4

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	894	0.75	0.78	64	empty
2	293	0.70	0.84	37	empty
3	138	0.59	0.84	19	empty
4	241	0.56	0.78	32	empty
5	215	0.52	0.76	19	empty

Compared structures

5DYK · Crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium falciparum… · 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 Q8MMZ4
Elsewhere: RCSB PDB 5DYK · PDBe 5DYK · UniProt Q8MMZ4

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