Research workbench
Crystal structure of apo C-cbl tkbd refined to 2.25 a resolution
Analyse Crystal structure of apo C-cbl tkbd refined to 2.25 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HKW
- Type
- protein
- Length
- 906 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl
- EC
- 6.3.2.-
- UniProt
- P22681
- Ligands
- NA
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | E3 ubiquitin-protein ligase cbl (EC 6.3.2.-) | protein | 302 | 59% helix, 9% strand | P22681 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.71 | 0.76 | 109 | empty |
| 2 | 528 | 0.65 | 0.76 | 50 | empty |
| 3 | 355 | 0.55 | 0.74 | 41 | empty |
| 4 | 161 | 0.51 | 0.79 | 21 | empty |
| 5 | 121 | 0.49 | 0.80 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–C · 755 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 752 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5HKW · Crystal Structure of Apo c-Cbl TKBD Refined to 2.25 A Resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P22681 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl (P22681) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P22681
- Elsewhere: RCSB PDB 5HKW · PDBe 5HKW · UniProt P22681
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.