Research workbench
Cryo-EM structure of ATP-bound fully inactive ampk in complex with Fab and nanobody
Analyse Cryo-EM structure of ATP-bound fully inactive ampk in complex with Fab and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JHH
- Type
- protein
- Length
- 1,698 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-AMP-activated protein kinase catalytic subunit alpha-1; 5'-AMP-activated protein…
- EC
- 2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26
- UniProt
- Q13131, O43741, P54619, C3SHQ8
- Ligands
- ATP, ADP, AMP, GLC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26) | protein | 379 | 35% helix, 20% strand | Q13131 |
| B | 5'-AMP-activated protein kinase subunit beta-2 | protein | 93 | 4% helix, 16% strand | O43741 |
| G | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 300 | 37% helix, 20% strand | P54619 |
| M | Maltodextrin-binding protein | protein | 367 | 44% helix, 19% strand | C3SHQ8 |
| L | Fab light chain | protein | 211 | 3% helix, 45% strand | — |
| H | Fab heavy chain | protein | 228 | 3% helix, 48% strand | — |
| N | Nanobody | protein | 120 | 3% helix, 47% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains G
- ADP · Adenosine-5'-diphosphate · ligand · chains G
- AMP · Adenosine monophosphate · ligand · chains G
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.86 | 0.87 | 97 | ATP, ADP, AMP |
| 2 | 645 | 0.79 | 0.84 | 58 | GLC |
| 3 | 297 | 0.69 | 0.83 | 32 | empty |
| 4 | 306 | 0.69 | 0.83 | 39 | empty |
| 5 | 606 | 0.65 | 0.75 | 67 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2397 Ų buried · 18 hydrogen bonds · protein-protein
- L–H · 2102 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 1385 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 1274 Ų buried · 14 hydrogen bonds · protein-protein
- B–G · 1192 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7JHH · Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody · the same entry in another collection · chain N against N, 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 G against A, TM-score 0.96
- 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 0.79
- Q13131 · 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 0.65
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 Q13131
- Every structure of UniProt O43741
- Every structure of UniProt P54619
- Every structure of UniProt C3SHQ8
- Elsewhere: RCSB PDB 7JHH · PDBe 7JHH · UniProt Q13131 · UniProt O43741 · UniProt P54619 · UniProt C3SHQ8
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