Research workbench
Structure of full length human ampk (non-phosphorylated at T-loop) in complex with a small molecule activator, a benzimidazole derivative (991)
Analyse Structure of full length human ampk (non-phosphorylated at T-loop) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ISO
- Type
- protein
- Length
- 1,835 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, 992
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 25% 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 | 453 | 39% helix, 20% strand | P54646 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 183 | 17% helix, 38% strand | Q9Y478 |
| E | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 298 | 42% helix, 23% strand | P54619 |
| C | 5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1, 2.7.11.27, 2.7.11.31) | protein | 429 | 35% helix, 21% strand | P54646 |
| D | 5'-AMP-activated protein kinase subunit beta-1 | protein | 173 | 12% helix, 41% strand | Q9Y478 |
| F | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 299 | 41% helix, 23% strand | P54619 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 6 copies · chains E, A, F, C
- STU · Staurosporine · ligand · 2 copies · chains A, C
- 992 · 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.83 | 0.85 | 82 | AMP |
| 2 | 1158 | 0.83 | 0.84 | 103 | AMP |
| 3 | 187 | 0.79 | 0.94 | 34 | empty |
| 4 | 1175 | 0.78 | 0.79 | 67 | empty |
| 5 | 1150 | 0.77 | 0.79 | 77 | empty |
Interfaces
10 interfaces between chains.
- A–B · 4214 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 4086 Ų buried · 42 hydrogen bonds · protein-protein
- A–E · 1671 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 1589 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 1218 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5ISO · Structure of full length human ampk (non-phosphorylated at T-loop) in complex with a… · 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 0.97
- P54646 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase catalytic subunit… · a predicted model of the same protein · chain C 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 D against A, TM-score 0.88
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 5ISO · PDBe 5ISO · UniProt P54646 · UniProt Q9Y478 · UniProt P54619
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