MolNFT v1 · #143511 · protein

Structure of full-length human ampk (A2B1G1) in complex with a small molecule activator SC4

6B1U · 5'-AMP-activated protein kinase catalytic subunit alpha-2: “Structure of full-length human ampk (A2B1G1) in complex with a small molecule activator SC4”. X-ray diffraction, 3 ligands (AMP, STU, CG7), 20 pockets (best druggability…

PDB: 6B1U
Type: protein
Length: 1,866 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-AMP-activated protein kinase catalytic subunit alpha-2; 5'-AMP-activated protein…
EC: 2.7.11.1, 2.7.11.27, 2.7.11.31
UniProt: P54646, Q9Y478, P54619
Ligands: AMP, STU, CG7
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1, 2.7.11.27, 2.7.11.31)	protein	442	39% helix, 20% strand	P54646
B	5'-AMP-activated protein kinase subunit beta-1	protein	184	14% helix, 38% strand	Q9Y478
C	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1, 2.7.11.27, 2.7.11.31)	protein	460	38% helix, 19% strand	P54646
D	5'-AMP-activated protein kinase subunit beta-1	protein	182	19% helix, 38% strand	Q9Y478
E	5'-AMP-activated protein kinase subunit gamma-1	protein	299	41% helix, 22% strand	P54619
F	5'-AMP-activated protein kinase subunit gamma-1	protein	299	41% helix, 23% strand	P54619

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 4 copies · chains A, E, C, F
STU · Staurosporine · ligand · 2 copies · chains A, C
CG7 · 5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid · ligand · 2 copies · chains A, B, C, D
IMD · Imidazole · additive · chains C

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	846	0.80	0.83	80	AMP
2	790	0.80	0.83	75	AMP
3	173	0.80	0.95	33	empty
4	190	0.78	0.93	39	empty
5	1056	0.76	0.78	87	empty

Interfaces

7 interfaces between chains.

A–B · 4195 Å² buried · 45 hydrogen bonds · protein-protein
C–D · 4188 Å² buried · 43 hydrogen bonds · protein-protein
C–F · 1702 Å² buried · 26 hydrogen bonds · protein-protein
A–E · 1570 Å² buried · 24 hydrogen bonds · protein-protein
B–E · 1246 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

6B1U · Structure of full-length human AMPK (a2b1g1) in complex with a small molecule activator… · the same entry in another collection · chain F against F, TM-score 1.00
P54619 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma-1… · a predicted model of the same protein · chain F against A, TM-score 0.97
P54646 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.94
Q9Y478 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-1… · a predicted model of the same protein · chain B against A, TM-score 0.85

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 P54646
Every structure of UniProt Q9Y478
Every structure of UniProt P54619
Elsewhere: RCSB PDB 6B1U · PDBe 6B1U · UniProt P54646 · UniProt Q9Y478 · UniProt P54619

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