Research workbench
Structure of the regulatory fragment of sccharomyces cerevisiae ampk in complex with AMP
Analyse Structure of the regulatory fragment of sccharomyces cerevisiae ampk in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TDH
- Type
- protein
- Length
- 559 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon catabolite-derepressing protein kinase; SNF1 protein kinase subunit beta-2…
- EC
- 2.7.11.1
- UniProt
- P06782, P34164, P12904
- Ligands
- AMP
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon catabolite-derepressing protein kinase (EC 2.7.11.1) | protein | 139 | 35% helix, 29% strand | P06782 |
| B | SNF1 protein kinase subunit beta-2 | protein | 104 | 36% helix, 27% strand | P34164 |
| C | Nuclear protein SNF4 | protein | 316 | 44% helix, 23% strand | P12904 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.82 | 0.87 | 59 | empty |
| 2 | 150 | 0.68 | 0.88 | 34 | AMP |
| 3 | 146 | 0.65 | 0.86 | 24 | empty |
| 4 | 52 | 0.48 | 0.86 | 16 | empty |
| 5 | 78 | 0.45 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2483 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1920 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1088 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3TDH · Structure of the regulatory fragment of sccharomyces cerevisiae AMPK in complex with AMP · the same entry in another collection · chain A against A, TM-score 1.00
- P12904 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma… · a predicted model of the same protein · chain C against A, TM-score 0.94
- P34164 · AlphaFold monomer V2.0 prediction for SNF1 protein kinase subunit beta-2 (P34164) · a predicted model of the same protein · chain B against A, TM-score 0.79
- P06782 · AlphaFold monomer V2.0 prediction for carbon catabolite-derepressing protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.73
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 P06782
- Every structure of UniProt P34164
- Every structure of UniProt P12904
- Elsewhere: RCSB PDB 3TDH · PDBe 3TDH · UniProt P06782 · UniProt P34164 · UniProt P12904
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