MolNFT v1 · #158638 · protein
Monobody (MC17) bound to tyrosine kinase binding domain of E3 ubiquitin ligase cbl
6O03 · E3 ubiquitin-protein ligase cbl: “Monobody (MC17) bound to tyrosine kinase binding domain of E3 ubiquitin ligase cbl”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #158638 on GenesisL1: 3D structure, binding…
- 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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