Research workbench
Functional construct of the Eukaryotic elongation factor 2 kinase bound to an ATP-competitive inhibitor
Analyse Functional construct of the Eukaryotic elongation factor 2 kinase bound to an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8GM4
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.12
- Source
- Homo sapiens
- Molecule
- Eukaryotic elongation factor 2 kinase; Calmodulin-1
- EC
- 2.7.11.20
- UniProt
- O00418, P0DP23
- Ligands
- ADP, EKI, CA, ZN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.12 · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic elongation factor 2 kinase (EC 2.7.11.20) | protein | 462 | 46% helix, 15% strand | O00418 |
| B | Calmodulin-1 | protein | 69 | 59% helix, 6% strand | P0DP23 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- EKI · 7-amino-1-cyclopropyl-3-ethyl-2,4-dioxo-1,2,3,4-tetrahydropyrido[2,3-d]pyrimidine-6-carboxamide · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.69 | 0.82 | 35 | empty |
| 2 | 338 | 0.63 | 0.79 | 37 | EKI |
| 3 | 256 | 0.61 | 0.80 | 36 | ADP |
| 4 | 132 | 0.51 | 0.80 | 21 | empty |
| 5 | 93 | 0.38 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1750 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- O00418 · AlphaFold monomer V2.0 prediction for eukaryotic elongation factor 2 kinase (O00418) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 O00418
- Every structure of UniProt P0DP23
- Elsewhere: RCSB PDB 8GM4 · PDBe 8GM4 · UniProt O00418 · UniProt P0DP23
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