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Structure of full length human ampk (A2B1G1) in complex with a small molecule activator MSG011

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: 7MYJ
Type: protein
Length: 1,877 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, 4O7, ZQV
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 31% 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	435	34% helix, 20% strand	P54646
B	5'-AMP-activated protein kinase subunit beta-1	protein	184	14% helix, 39% 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	465	37% helix, 18% strand	P54646
D	5'-AMP-activated protein kinase subunit beta-1	protein	187	13% helix, 37% strand	Q9Y478
E, F	5'-AMP-activated protein kinase subunit gamma-1	protein	303	40% helix, 21% strand	P54619

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 4 copies · chains E, A, F, C
4O7 · (5s,6r,7r,9r,13cr,14r,16as)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,14,15,16,16A-octahydro-5h,13ch-5,9-epoxy-4B,9A,1 5-triazadibenzo[b,h]cyclonona[1,2,3, 4-jkl]cyclopenta[e]-as-indacen-14-ol · ligand · 2 copies · chains A, C
ZQV · 5-({5-[(4'R)-4'-acetamido-2',3',4',5'-tetrahydro[1,1'-biphenyl]-4-yl]-6-chloro-1H-imidazo[4,5-b]pyridin-2-yl}oxy)-2-methylbenzoic acid · ligand · 2 copies · chains A, B, C, D

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	999	0.85	0.85	104	AMP
2	242	0.79	0.92	38	empty
3	732	0.76	0.81	69	AMP
4	937	0.75	0.78	73	empty
5	971	0.72	0.76	70	empty

Interfaces

7 interfaces between chains.

A–B · 4351 Å² buried · 47 hydrogen bonds · protein-protein
C–D · 4147 Å² buried · 45 hydrogen bonds · protein-protein
C–F · 1666 Å² buried · 27 hydrogen bonds · protein-protein
A–E · 1641 Å² buried · 25 hydrogen bonds · protein-protein
B–E · 1267 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

7MYJ · 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 E against A, TM-score 0.96
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 0.95
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 0.86

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 7MYJ · PDBe 7MYJ · UniProt P54646 · UniProt Q9Y478 · UniProt P54619

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