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Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor GP5A
Analyse Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZJB
- Type
- protein
- Length
- 1,300 residues
- Chains
- 6
- 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
- G5P, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10) | protein | 217 | 48% helix, 17% strand | Q9UIJ7 |
| C | GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10) | protein | 216 | 49% helix, 17% strand | Q9UIJ7 |
| D | GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10) | protein | 218 | 48% helix, 18% strand | Q9UIJ7 |
| E, F | GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10) | protein | 216 | 48% helix, 17% strand | Q9UIJ7 |
Ligands and binding sites
- G5P · P1-(5'-adenosyl)-P5-(5'-guanosyl) pentaphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.81 | 0.89 | 51 | G5P, MG |
| 2 | 469 | 0.80 | 0.88 | 52 | G5P, MG |
| 3 | 473 | 0.80 | 0.88 | 53 | G5P, MG |
| 4 | 630 | 0.79 | 0.85 | 58 | G5P, MG |
| 5 | 542 | 0.78 | 0.85 | 63 | G5P, MG |
Interfaces
7 interfaces between chains.
- B–D · 614 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 566 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 540 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 309 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 142 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZJB · Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UIJ7 · AlphaFold monomer V2.0 prediction for GTP:AMP phosphotransferase AK3, mitochondrial… · a predicted model of the same protein · chain E against A, TM-score 0.97
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 6ZJB · PDBe 6ZJB · UniProt Q9UIJ7
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