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BETA1 carbohydrate binding module (cbm) of AMP-activated protein kinase (ampk) in complex with glucosyl-beta-cyclododextrin
Analyse BETA1 carbohydrate binding module (cbm) of AMP-activated protein kinase (ampk)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YEF
- Type
- protein
- Length
- 559 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-AMP-activated protein kinase subunit beta-1
- UniProt
- P80386
- Ligands
- GLC, SO4
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-AMP-activated protein kinase subunit beta-1 | protein | 80 | 4% helix, 55% strand | P80386 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 86 | 8% helix, 52% strand | P80386 |
| C | 5'-AMP-activated protein kinase subunit beta-1 | protein | 79 | 4% helix, 56% strand | P80386 |
| D, F | 5'-AMP-activated protein kinase subunit beta-1 | protein | 77 | 4% helix, 53% strand | P80386 |
| E | 5'-AMP-activated protein kinase subunit beta-1 | protein | 85 | 8% helix, 52% strand | P80386 |
| G | 5'-AMP-activated protein kinase subunit beta-1 | protein | 75 | 4% helix, 49% strand | P80386 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 49 copies · chains A, D, B, C, F, E, G
- SO4 · Sulfate ion · ion · 6 copies · chains B, D, E, F
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.42 | 0.73 | 30 | GLC, SO4 |
| 2 | 128 | 0.39 | 0.74 | 19 | GLC |
| 3 | 56 | 0.30 | 0.75 | 21 | empty |
| 4 | 63 | 0.30 | 0.74 | 22 | empty |
Interfaces
8 interfaces between chains.
- B–C · 623 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 614 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 9 hydrogen bonds · protein-protein
- D–G · 359 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 162 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YEF · beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex… · the same entry in another collection · chain G against G, TM-score 1.00
- P80386 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-1… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P80386
- Elsewhere: RCSB PDB 4YEF · PDBe 4YEF · UniProt P80386
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