Research workbench
Structure of PHOSPHOTYR371-C-cbl-UBCH5B complex
Analyse Structure of PHOSPHOTYR371-C-cbl-UBCH5B complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A49
- Type
- protein
- Length
- 223 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl; Ubiquitin-conjugating enzyme E2 D2
- EC
- 2.3.2.27, 2.3.2.23, 2.3.2.24
- UniProt
- P22681, P62837
- Ligands
- ZN, K
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase cbl (EC 2.3.2.27) | protein | 77 | 23% helix, 23% strand | P22681 |
| B | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 146 | 36% helix, 21% strand | P62837 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.42 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 712 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4A49 · Structure of phosphoTyr371-c-Cbl-UbcH5B complex · the same entry in another collection · chain A against A, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.94
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 P62837
- Elsewhere: RCSB PDB 4A49 · PDBe 4A49 · UniProt P22681 · UniProt P62837
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