MolNFT v1 · #51880 · protein

Structure of the PDK1 pH domain K465E mutant

2VKI · 3-phopshoinositide dependent protein kinase 1: “Structure of the PDK1 pH domain K465E mutant”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.48). MolNFT v1 #51880 on GenesisL1: 3D structure, binding sites and…

PDB: 2VKI
Type: protein
Length: 139 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-phopshoinositide dependent protein kinase 1
EC: 2.7.11.1
UniProt: O15530
Ligands: SO4
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-phopshoinositide dependent protein kinase 1 (EC 2.7.11.1)	protein	139	27% helix, 39% strand	O15530

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	67	0.48	0.84	15	empty
2	86	0.39	0.77	13	empty
3	64	0.36	0.78	16	empty

Compared structures

2VKI · Structure of the PDK1 PH domain K465E mutant · the same entry in another collection · chain A against A, TM-score 1.00
O15530 · AlphaFold monomer V2.0 prediction for 3-phosphoinositide-dependent protein kinase 1… · a predicted model of the same protein · chain A against A, TM-score 0.93

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 O15530
Elsewhere: RCSB PDB 2VKI · PDBe 2VKI · UniProt O15530

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