MolNFT v1 · #90145 · protein
Co-crystal structure of an chimeric ampk core with ATP
4EAG · EG:132E8.2 protein: “Co-crystal structure of an chimeric ampk core with ATP”. X-ray diffraction, 2 ligands (ATP, TAM), 7 pockets (best druggability 0.78). MolNFT v1 #90145 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4EAG
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EG:132E8.2 protein; 5'-AMP-activated protein kinase subunit beta-1; 5'-AMP-activated…
- EC
- 2.7.11.-, 2.7.11.16
- UniProt
- O18645, P80386, P80385
- Ligands
- ATP, TAM
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EG:132E8.2 protein (EC 2.7.11.-, 2.7.11.16) | protein | 98 | 32% helix, 35% strand | O18645 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 58 | 0% helix, 53% strand | P80386 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 289 | 41% helix, 24% strand | P80385 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.78 | 0.80 | 95 | ATP, TAM |
| 2 | 116 | 0.56 | 0.84 | 28 | empty |
| 3 | 61 | 0.52 | 0.86 | 11 | empty |
| 4 | 99 | 0.40 | 0.76 | 21 | empty |
| 5 | 63 | 0.39 | 0.79 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1861 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 922 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4EAG · Co-crystal structure of an chimeric AMPK core with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- P80385 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma-1… · a predicted model of the same protein · chain C against A, TM-score 0.94
- P80386 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-1… · a predicted model of the same protein · chain B against A, TM-score 0.85
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 O18645
- Every structure of UniProt P80386
- Every structure of UniProt P80385
- Elsewhere: RCSB PDB 4EAG · PDBe 4EAG · UniProt O18645 · UniProt P80386 · UniProt P80385
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