Research workbench
Structure of full length human ampk (A2B2G1) in complex with a small molecule activator SC4.
Analyse Structure of full length human ampk (A2B2G1) 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
- 6B2E
- Type
- protein
- Length
- 931 residues
- Chains
- 3
- 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, O43741, P54619
- Ligands
- AMP, STU, CG7, GLC
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% 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 | 443 | 37% helix, 19% strand | P54646 |
| B | 5'-AMP-activated protein kinase subunit beta-2 | protein | 193 | 10% helix, 32% strand | O43741 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 295 | 38% helix, 19% strand | P54619 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C
- STU · Staurosporine · ligand · chains A
- 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 · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 7 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.82 | 0.87 | 75 | AMP |
| 2 | 410 | 0.72 | 0.83 | 42 | empty |
| 3 | 227 | 0.69 | 0.85 | 49 | empty |
| 4 | 499 | 0.69 | 0.79 | 64 | AMP |
| 5 | 465 | 0.68 | 0.79 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3964 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1129 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 959 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6B2E · Structure of full length human AMPK (a2b2g1) in complex with a small molecule activator… · the same entry in another collection · chain A against A, 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 C 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
- O43741 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-2… · 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
- Every structure of UniProt O43741
- Every structure of UniProt P54619
- Elsewhere: RCSB PDB 6B2E · PDBe 6B2E · UniProt P54646 · UniProt O43741 · UniProt P54619
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