MolNFT v1 · #171868 · protein
Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor ATP
6ZJD · GTP:AMP phosphotransferase AK3, mitochondrial: “Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor ATP”. X-ray diffraction, 4 ligands (ATP, MG, NA), 2 pockets (best druggability 0.55). MolNFT v1 #171868 on…
- PDB
- 6ZJD
- Type
- protein
- Length
- 214 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP:AMP phosphotransferase AK3, mitochondrial
- EC
- 2.7.4.10
- UniProt
- Q9UIJ7
- Ligands
- ATP, MG, NA, CL
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10) | protein | 214 | 47% helix, 18% strand | Q9UIJ7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.55 | 0.77 | 35 | ATP, MG, CL |
| 2 | 140 | 0.47 | 0.77 | 18 | empty |
Compared structures
- 6ZJD · Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor ATP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UIJ7 · AlphaFold monomer V2.0 prediction for GTP:AMP phosphotransferase AK3, mitochondrial… · a predicted model of the same protein · chain A 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 Q9UIJ7
- Elsewhere: RCSB PDB 6ZJD · PDBe 6ZJD · UniProt Q9UIJ7
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