Research workbench
Structure of modified PHOSPHOTYR371-C-cbl-UBCH5B-zap-70 complex
Analyse Structure of modified PHOSPHOTYR371-C-cbl-UBCH5B-zap-70 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A4B
- Type
- protein
- Length
- 543 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl; Tyrosine-protein kinase zap-70; Ubiquitin-conjugating…
- EC
- 6.3.2.-, 2.7.10.2, 6.3.2.19
- UniProt
- P22681, P43403, P62837
- Ligands
- ZN, CA
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase cbl (EC 6.3.2.-) | protein | 388 | 50% helix, 10% strand | P22681 |
| B | Tyrosine-protein kinase zap-70 (EC 2.7.10.2) | protein | 9 | 0% helix, 11% strand | P43403 |
| C | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 146 | 37% helix, 21% strand | P62837 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.60 | 0.77 | 42 | empty |
| 2 | 151 | 0.53 | 0.80 | 21 | empty |
| 3 | 164 | 0.49 | 0.77 | 24 | empty |
| 4 | 124 | 0.42 | 0.76 | 21 | empty |
| 5 | 64 | 0.31 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 591 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4A4B · Structure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 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 C 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 0.99
- P43403 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase zap-70 (P43403) · a predicted model of the same protein · chain B against A, TM-score 0.60
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 P43403
- Every structure of UniProt P62837
- Elsewhere: RCSB PDB 4A4B · PDBe 4A4B · UniProt P22681 · UniProt P43403 · UniProt P62837
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