MolNFT v1 · #84525 · protein
Structure of PHOSPHOTYR363-cbl-B - UBCH5B-ub - zap-70 peptide complex
3ZNI · E3 ubiquitin-protein ligase cbl-B: “Structure of PHOSPHOTYR363-cbl-B - UBCH5B-ub - zap-70 peptide complex”. X-ray diffraction, 2 ligands (ZN, CA), 20 pockets (best druggability 0.78). MolNFT v1 #84525 on GenesisL1: 3D structure…
- PDB
- 3ZNI
- Type
- protein
- Length
- 2,482 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl-B; Tyrosine-protein kinase zap-70; Ubiquitin-conjugating…
- EC
- 6.3.2.19, 2.7.10.2
- UniProt
- Q13191, P43403, P62837, P0CG48
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, M | E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.19) | protein | 390 | 51% helix, 11% strand | Q13191 |
| B, N | Tyrosine-protein kinase zap-70 (EC 2.7.10.2) | protein | 9 | 0% helix, 11% strand | P43403 |
| C, G, K, O | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 146 | 36% helix, 22% strand | P62837 |
| D, H, L, P | Polyubiquitin-C | protein | 77 | 19% helix, 36% strand | P0CG48 |
| F, J | Tyrosine-protein kinase zap-70 (EC 2.7.10.2) | protein | 8 | 0% helix, 13% strand | P43403 |
| I | E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.19) | protein | 386 | 52% helix, 11% strand | Q13191 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, E, I, M
- CA · Calcium ion · metal · 4 copies · chains A, E, I, M
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, E, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.78 | 0.95 | 29 | empty |
| 2 | 111 | 0.75 | 0.95 | 24 | empty |
| 3 | 893 | 0.72 | 0.77 | 80 | empty |
| 4 | 896 | 0.72 | 0.77 | 81 | empty |
| 5 | 220 | 0.71 | 0.87 | 40 | empty |
Interfaces
26 interfaces between chains.
- O–P · 993 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 973 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 938 Ų buried · 22 hydrogen bonds · protein-protein
- K–L · 931 Ų buried · 22 hydrogen bonds · protein-protein
- E–O · 782 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 isopeptide (phosphorylation, isopeptide).
Compared structures
- 3ZNI · Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex · the same entry in another collection · chain P against P, TM-score 1.00
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 Q13191
- Every structure of UniProt P43403
- Every structure of UniProt P62837
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 3ZNI · PDBe 3ZNI · UniProt Q13191 · UniProt P43403 · UniProt P62837 · UniProt P0CG48
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