Research workbench
The crystal structure of the pH domain of human AKT3 protein kinase
Analyse The crystal structure of the pH domain of human AKT3 protein kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X18
- Type
- protein
- Length
- 913 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rac-gamma SERINE/THREONINE-protein kinase
- EC
- 2.7.11.1
- UniProt
- Q9Y243
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rac-gamma SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 111 | 23% helix, 39% strand | Q9Y243 |
| B | Rac-gamma SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 114 | 25% helix, 43% strand | Q9Y243 |
| C, D, G | Rac-gamma SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 115 | 25% helix, 43% strand | Q9Y243 |
| E, H | Rac-gamma SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 116 | 22% helix, 37% strand | Q9Y243 |
| F | Rac-gamma SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 111 | 20% helix, 39% strand | Q9Y243 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, E, F, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.81 | 0.82 | 128 | empty |
| 2 | 394 | 0.68 | 0.81 | 62 | empty |
| 3 | 659 | 0.68 | 0.76 | 63 | EPE |
| 4 | 262 | 0.61 | 0.80 | 34 | empty |
| 5 | 217 | 0.58 | 0.80 | 36 | empty |
Interfaces
16 interfaces between chains.
- D–H · 511 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 480 Ų buried · 4 hydrogen bonds · protein-protein
- F–H · 435 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 431 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 429 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2X18 · The crystal structure of the PH domain of human AKT3 protein kinase · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y243 · AlphaFold monomer V2.0 prediction for rac-gamma SERINE/THREONINE- protein kinase (Q9Y243) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9Y243
- Elsewhere: RCSB PDB 2X18 · PDBe 2X18 · UniProt Q9Y243
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