Research workbench
Structure of gak kinase in complex with a nanobody
Analyse Structure of gak kinase in complex with a nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C57
- Type
- protein
- Length
- 866 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
- FEF, SO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-G-associated kinase (EC 2.7.11.1) | protein | 310 | 39% helix, 20% strand | O14976 |
| B | Cyclin-G-associated kinase (EC 2.7.11.1) | protein | 308 | 38% helix, 20% strand | O14976 |
| C | Nanobody | protein | 127 | 7% helix, 48% strand | — |
| D | Nanobody | protein | 121 | 7% helix, 50% strand | — |
Ligands and binding sites
- FEF · (2Z,3E)-2,3'-biindole-2',3(1H,1'H)-dione 3-{O-[(3R)-3,4-dihydroxybutyl]oxime} · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.81 | 0.83 | 112 | FEF |
| 2 | 341 | 0.74 | 0.86 | 53 | EDO |
| 3 | 182 | 0.65 | 0.85 | 28 | FEF |
| 4 | 155 | 0.47 | 0.76 | 19 | empty |
| 5 | 139 | 0.42 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 741 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 733 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 541 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 4C57 · PDBe 4C57 · UniProt O14976
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.