Research workbench
Crystal structure of Akt1 (aa 123-480) kinase with a bisubstrate
Analyse Crystal structure of Akt1 (aa 123-480) kinase with a bisubstrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NPZ
- Type
- protein
- Length
- 665 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.12
- Source
- Homo sapiens
- Molecule
- RAC-alpha serine/threonine-protein kinase; bisubstrate
- EC
- 2.7.11.1
- UniProt
- P31749
- Ligands
- MN, VO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.12 · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAC-alpha serine/threonine-protein kinase (EC 2.7.11.1) | protein | 322 | 36% helix, 17% strand | P31749 |
| B | RAC-alpha serine/threonine-protein kinase (EC 2.7.11.1) | protein | 323 | 36% helix, 16% strand | P31749 |
| F, G | bisubstrate | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, F, G
- VO4 · Vanadate ion · ion
- PGE · Triethylene glycol · additive · 2 copies · chains A, F
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.73 | 0.96 | 21 | empty |
| 2 | 73 | 0.71 | 0.96 | 22 | empty |
| 3 | 274 | 0.52 | 0.75 | 36 | PGE, MN |
| 4 | 55 | 0.45 | 0.84 | 13 | empty |
| 5 | 76 | 0.43 | 0.80 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–G · 1087 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 1052 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 228 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation, nonstandard).
Compared structures
- 6NPZ · Crystal structure of AKT1 (aa 123-480) kinase with a bisubstrate · the same entry in another collection · chain A against A, TM-score 1.00
- P31749 · AlphaFold monomer V2.0 prediction for rac-alpha SERINE/THREONINE- protein kinase (P31749) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P31749
- Elsewhere: RCSB PDB 6NPZ · PDBe 6NPZ · UniProt P31749
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