Research workbench
Crystal structure of cbl-C (cbl-3) tkb domain in complex with EGFR PY1069 peptide
Analyse Crystal structure of cbl-C (cbl-3) tkb domain in complex with EGFR PY1069… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OP0
- Type
- protein
- Length
- 662 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal transduction protein cbl-C; Epidermal growth factor receptor
- UniProt
- Q9ULV8, P00533
- Ligands
- NA, NI
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Signal transduction protein cbl-C | protein | 321 | 55% helix, 8% strand | Q9ULV8 |
| C, D | Epidermal growth factor receptor | protein | 10 | 0% helix, 10% strand | P00533 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.79 | 0.83 | 95 | empty |
| 2 | 145 | 0.50 | 0.79 | 24 | empty |
| 3 | 53 | 0.48 | 0.86 | 15 | empty |
| 4 | 55 | 0.47 | 0.85 | 15 | empty |
| 5 | 96 | 0.34 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 838 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 597 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 596 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation, phosphorylation).
Compared structures
- 3OP0 · Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide · the same entry in another collection · chain D against D, TM-score 1.00
- Q9ULV8 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl-C (Q9ULV8) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain D against A, TM-score 0.44
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 Q9ULV8
- Every structure of UniProt P00533
- Elsewhere: RCSB PDB 3OP0 · PDBe 3OP0 · UniProt Q9ULV8 · UniProt P00533
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