MolNFT v1 · #79485 · protein
Structure of the regulatory fragment of saccharomyces cerevisiae ampk in complex with ADP
3T4N · Carbon catabolite-derepressing protein kinase: “Structure of the regulatory fragment of saccharomyces cerevisiae ampk in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 3 pockets (best druggability 0.78). MolNFT v1 #79485 on…
- PDB
- 3T4N
- Type
- protein
- Length
- 554 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
- ADP
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon catabolite-derepressing protein kinase (EC 2.7.11.1) | protein | 139 | 37% helix, 29% strand | P06782 |
| B | SNF1 protein kinase subunit beta-2 | protein | 104 | 37% helix, 26% strand | P34164 |
| C | Nuclear protein SNF4 | protein | 311 | 47% helix, 23% strand | P12904 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.78 | 0.85 | 70 | ADP |
| 2 | 520 | 0.77 | 0.84 | 50 | empty |
| 3 | 110 | 0.40 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2576 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1941 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1016 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3T4N · Structure of the regulatory fragment of Saccharomyces cerevisiae AMPK in complex with ADP · 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 3T4N · PDBe 3T4N · UniProt P06782 · UniProt P34164 · UniProt P12904
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