MolNFT v1 · #113954 · protein
Crystal structure of cbl-B tkb domain in complex with cblin
5AXI · E3 ubiquitin-protein ligase cbl-B: “Crystal structure of cbl-B tkb domain in complex with cblin”. X-ray diffraction, 2 ligands (CA, CL), 12 pockets (best druggability 0.80). MolNFT v1 #113954 on GenesisL1: 3D structure, binding…
- PDB
- 5AXI
- Type
- protein
- Length
- 911 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl-B; Cblin
- EC
- 6.3.2.-
- UniProt
- Q3TTA7
- Ligands
- CA, CL
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.-) | protein | 305 | 60% helix, 9% strand | Q3TTA7 |
| B | E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.-) | protein | 302 | 60% helix, 8% strand | Q3TTA7 |
| C | E3 ubiquitin-protein ligase cbl-B (EC 6.3.2.-) | protein | 299 | 58% helix, 10% strand | Q3TTA7 |
| E | Cblin | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.80 | 0.81 | 93 | empty |
| 2 | 152 | 0.64 | 0.86 | 21 | empty |
| 3 | 216 | 0.60 | 0.81 | 34 | empty |
| 4 | 187 | 0.54 | 0.78 | 30 | empty |
| 5 | 66 | 0.49 | 0.85 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1433 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 503 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 414 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5AXI · Crystal structure of Cbl-b TKB domain in complex with Cblin · the same entry in another collection · chain C against C, TM-score 1.00
- Q3TTA7 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl-B (Q3TTA7) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q3TTA7
- Elsewhere: RCSB PDB 5AXI · PDBe 5AXI · UniProt Q3TTA7
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