Research workbench
Structure of C-cbl-zap-70 peptide complex
Analyse Structure of C-cbl-zap-70 peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y1N
- Type
- protein
- Length
- 775 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase; Tyrosine-protein kinase zap-70 zap-70,70 kda zeta-associated…
- EC
- 6.3.2.-, 2.7.10.2
- UniProt
- P22681, P43403
- Ligands
- ZN, CA
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase (EC 6.3.2.-) | protein | 377 | 52% helix, 10% strand | P22681 |
| B, D | Tyrosine-protein kinase zap-70 zap-70,70 kda zeta-associated protein, syk-related tyrosine kinase (EC 2.7.10.2) | protein | 9 | 0% helix, 11% strand | P43403 |
| C | E3 ubiquitin-protein ligase (EC 6.3.2.-) | protein | 380 | 50% helix, 10% strand | P22681 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.72 | 0.97 | 24 | empty |
| 2 | 52 | 0.70 | 0.98 | 18 | empty |
| 3 | 352 | 0.67 | 0.81 | 40 | empty |
| 4 | 394 | 0.65 | 0.79 | 42 | empty |
| 5 | 57 | 0.62 | 0.93 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 662 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 643 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 502 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2Y1N · Structure of c-Cbl-ZAP-70 peptide complex · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.83
- 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 0.41
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
- Elsewhere: RCSB PDB 2Y1N · PDBe 2Y1N · UniProt P22681 · UniProt P43403
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