Research workbench
Monobody (MC17) bound to tyrosine kinase binding domain of E3 ubiquitin ligase cbl
Analyse Monobody (MC17) bound to tyrosine kinase binding domain of E3 ubiquitin ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O03
- Type
- protein
- Length
- 774 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl; Monobody (MC17)
- EC
- 2.3.2.27
- UniProt
- P22681
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | E3 ubiquitin-protein ligase cbl (EC 2.3.2.27) | protein | 302 | 57% helix, 9% strand | P22681 |
| C, D | Monobody (MC17) | protein | 87 | 0% helix, 57% strand | — |
| A | E3 ubiquitin-protein ligase cbl (EC 2.3.2.27) | protein | 298 | 57% helix, 9% strand | P22681 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.73 | 0.76 | 101 | empty |
| 2 | 378 | 0.69 | 0.82 | 43 | empty |
| 3 | 222 | 0.68 | 0.85 | 34 | empty |
| 4 | 182 | 0.50 | 0.77 | 26 | empty |
| 5 | 129 | 0.45 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1031 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1012 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 242 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 215 Ų buried · 1 hydrogen bond · protein-protein
- C–A · 172 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6O03 · Monobody (MC17) bound to tyrosine kinase binding domain of E3 ubiquitin ligase CBL · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.97
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 6O03 · PDBe 6O03 · UniProt P22681
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