Research workbench
Crystal structure of cbl-B tkb domain in complex with EGFR PY1069 peptide
Analyse Crystal structure of cbl-B tkb domain in complex with EGFR PY1069 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PFV
- Type
- protein
- Length
- 633 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl-B; 11-meric peptide from epidermal growth factor receptor
- EC
- 6.3.2.-
- UniProt
- Q13191, P00533
- Ligands
- NA, SO4, CL
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.-) | protein | 302 | 61% helix, 8% strand | Q13191 |
| B | E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.-) | protein | 310 | 59% helix, 8% strand | Q13191 |
| C | 11-meric peptide from epidermal growth factor receptor | protein | 10 | 0% helix, 10% strand | P00533 |
| D | 11-meric peptide from epidermal growth factor receptor | protein | 11 | 0% helix, 9% strand | P00533 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.68 | 0.85 | 34 | EDO, PG4 |
| 2 | 290 | 0.67 | 0.82 | 41 | EDO, SO4 |
| 3 | 122 | 0.61 | 0.86 | 19 | empty |
| 4 | 144 | 0.60 | 0.84 | 20 | empty |
| 5 | 130 | 0.53 | 0.82 | 20 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 770 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 627 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 589 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3PFV · Crystal structure of Cbl-b TKB domain in complex with EGFR pY1069 peptide · the same entry in another collection · chain D against D, TM-score 1.00
- Q13191 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl-B (Q13191) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain C against A, TM-score 0.39
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 Q13191
- Every structure of UniProt P00533
- Elsewhere: RCSB PDB 3PFV · PDBe 3PFV · UniProt Q13191 · UniProt P00533
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