MolNFT v1 · #31119 · protein
The three-dimensional structure of the complex between mitochondrial matrix adenylate kinase and its substrate AMP at 1.85 ångströms resolution
2AK3 · Adenylate kinase isoenzyme-3: “The three-dimensional structure of the complex between mitochondrial matrix adenylate kinase and its…”. X-ray diffraction, 2 ligands (AMP, SO4), 4 pockets (best druggability 0.58). MolNFT v1 #31119 on…
- PDB
- 2AK3
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase isoenzyme-3
- EC
- 2.7.4.10
- UniProt
- P08760
- Ligands
- AMP, SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase isoenzyme-3 (EC 2.7.4.10) | protein | 226 | 46% helix, 17% strand | P08760 |
| B | Adenylate kinase isoenzyme-3 (EC 2.7.4.10) | protein | 220 | 47% helix, 17% strand | P08760 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.58 | 0.77 | 36 | SO4, AMP |
| 2 | 257 | 0.55 | 0.77 | 31 | AMP |
| 3 | 85 | 0.45 | 0.80 | 18 | empty |
| 4 | 91 | 0.44 | 0.79 | 18 | empty |
Compared structures
- 2AK3 · The three-dimensional structure of the complex between mitochondrial matrix adenylate… · the same entry in another collection · chain A against A, TM-score 1.00
- P08760 · AlphaFold monomer V2.0 prediction for GTP:AMP phosphotransferase AK3, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.76
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 P08760
- Elsewhere: RCSB PDB 2AK3 · PDBe 2AK3 · UniProt P08760
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