Research workbench
Structure of a cbl-UBCH7 complex: ring domain function in ubiquitin- protein ligases
Analyse Structure of a cbl-UBCH7 complex: ring domain function in ubiquitin- protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FBV
- Type
- protein
- Length
- 541 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal transduction protein cbl; Zap-70 peptide; Ubiquitin-conjugating enzyme E12-18 kda…
- EC
- 6.3.2.19
- UniProt
- P22681, P68036
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal transduction protein cbl | protein | 388 | 50% helix, 8% strand | P22681 |
| B | Zap-70 peptide | protein | 9 | 0% helix, 0% strand | — |
| C | Ubiquitin-conjugating enzyme E12-18 kda UBCH7 (EC 6.3.2.19) | protein | 144 | 24% helix, 15% strand | P68036 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.73 | 0.96 | 25 | empty |
| 2 | 708 | 0.69 | 0.77 | 84 | SO4 |
| 3 | 139 | 0.61 | 0.85 | 27 | empty |
| 4 | 61 | 0.34 | 0.78 | 18 | SO4 |
| 5 | 77 | 0.29 | 0.72 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 934 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 645 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 1FBV · Structure of a cbl-UBCH7 complex: ring domain function in ubiquitin-protein ligases · the same entry in another collection · chain A against A, TM-score 1.00
- P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain C against A, TM-score 0.92
- 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 0.81
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
- Every structure of UniProt P68036
- Elsewhere: RCSB PDB 1FBV · PDBe 1FBV · UniProt P22681 · UniProt P68036
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