Research workbench
Crystal structure of the heterotrimer core of the S. cerevisiae ampk homolog SNF1
Analyse Crystal structure of the heterotrimer core of the S. cerevisiae ampk homolog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QLV
- Type
- protein
- Length
- 1,181 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon catabolite derepressing protein kinase; Protein SIP2; Nuclear protein SNF4
- EC
- 2.7.11.1
- UniProt
- P06782, P34164, P12904
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Carbon catabolite derepressing protein kinase (EC 2.7.11.1) | protein | 133 | 39% helix, 26% strand | P06782 |
| B | Protein SIP2 | protein | 155 | 11% helix, 43% strand | P34164 |
| C, F | Nuclear protein SNF4 | protein | 310 | 41% helix, 21% strand | P12904 |
| E | Protein SIP2 | protein | 140 | 2% helix, 49% strand | P34164 |
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 | 781 | 0.86 | 0.88 | 96 | empty |
| 2 | 806 | 0.84 | 0.87 | 91 | empty |
| 3 | 77 | 0.70 | 0.94 | 17 | empty |
| 4 | 80 | 0.70 | 0.94 | 18 | empty |
| 5 | 233 | 0.69 | 0.86 | 35 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1888 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1696 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1665 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1661 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1481 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2QLV · Crystal structure of the heterotrimer core of the S. cerevisiae AMPK homolog SNF1 · the same entry in another collection · chain F against F, 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 0.96
- 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 0.67
- P34164 · AlphaFold monomer V2.0 prediction for SNF1 protein kinase subunit beta-2 (P34164) · a predicted model of the same protein · chain E against A, TM-score 0.64
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 2QLV · PDBe 2QLV · UniProt P06782 · UniProt P34164 · UniProt P12904
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