Research workbench

AKT1 with AMP-pnp

Analyse AKT1 with AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EKK
Type: protein
Length: 658 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rac-alpha SERINE/THREONINE-protein kinase; Glycogen synthase kinase-3 beta
EC: 2.7.11.1, 2.7.11.26
UniProt: P31749, P49841
Ligands: ANP, MN
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Rac-alpha SERINE/THREONINE-protein kinase (EC 2.7.11.1)	protein	319	32% helix, 17% strand	P31749
C, D	Glycogen synthase kinase-3 beta (EC 2.7.11.26, 2.7.11.1)	protein	10	0% helix, 20% strand	P49841

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, C, B, D
MN · Manganese (II) ion · metal · 4 copies · chains A, C, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	353	0.81	0.90	42	ANP, MN
2	413	0.80	0.89	50	ANP, MN
3	312	0.56	0.76	33	empty
4	65	0.41	0.80	15	empty
5	62	0.39	0.80	15	empty

Interfaces

4 interfaces between chains.

A–C · 722 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 720 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 215 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 24 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

4EKK · Akt1 with AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
P31749 · AlphaFold monomer V2.0 prediction for rac-alpha SERINE/THREONINE- protein kinase (P31749) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P31749
Every structure of UniProt P49841
Elsewhere: RCSB PDB 4EKK · PDBe 4EKK · UniProt P31749 · UniProt P49841

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