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
- 5Y7Z
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- 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, SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclin-G-associated kinase (EC 2.7.11.1) | protein | 312 | 37% helix, 19% strand | O14976 |
| D | Nanobody | protein | 124 | 5% helix, 50% strand | — |
| C | Nanobody | protein | 122 | 5% helix, 50% strand | — |
Ligands and binding sites
- IRE · Gefitinib · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.77 | 0.82 | 62 | IRE |
| 2 | 603 | 0.75 | 0.82 | 69 | empty |
| 3 | 763 | 0.74 | 0.79 | 71 | IRE, SO4 |
| 4 | 144 | 0.52 | 0.80 | 20 | SO4 |
| 5 | 100 | 0.50 | 0.81 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–C · 914 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 904 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 311 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5Y7Z · 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 0.99
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 5Y7Z · PDBe 5Y7Z · UniProt O14976
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