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

Analyse Structure of full-length human ampk (A2B1G1) in complex with a small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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

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