Research workbench
Complex structure of cyclin G-associated kinase with gefitinib
Analyse Complex structure of cyclin G-associated kinase with gefitinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y80
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-G-associated kinase; Nanobody
- EC
- 2.7.11.1
- UniProt
- O14976
- Ligands
- IRE
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-G-associated kinase (EC 2.7.11.1) | protein | 306 | 36% helix, 19% strand | O14976 |
| B | Nanobody | protein | 124 | 7% helix, 47% strand | — |
Ligands and binding sites
- IRE · Gefitinib · ligand · 2 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 | 749 | 0.75 | 0.80 | 84 | IRE |
| 2 | 128 | 0.47 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 721 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5Y80 · Complex structure of cyclin G-associated kinase with gefitinib · the same entry in another collection · chain A against A, TM-score 1.00
- O14976 · AlphaFold monomer V2.0 prediction for cyclin-G-associated kinase (O14976) · 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 O14976
- Elsewhere: RCSB PDB 5Y80 · PDBe 5Y80 · UniProt O14976
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