MolNFT v1 · #115034 · protein
Crystal structure of E3 ligase itch with a ub variant
5C7M · E3 ubiquitin-protein ligase itchy homolog: “Crystal structure of E3 ligase itch with a ub variant”. X-ray diffraction, 5 pockets (best druggability 0.77). MolNFT v1 #115034 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5C7M
- Type
- protein
- Length
- 514 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase itchy homolog; Polyubiquitin-C
- EC
- 6.3.2.-
- UniProt
- Q96J02, P0CG48
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase itchy homolog (EC 6.3.2.-) | protein | 370 | 50% helix, 12% strand | Q96J02 |
| B | Polyubiquitin-C | protein | 73 | 16% helix, 33% strand | P0CG48 |
| C | Polyubiquitin-C | protein | 71 | 21% helix, 35% strand | P0CG48 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.77 | 0.82 | 69 | empty |
| 2 | 315 | 0.71 | 0.84 | 53 | empty |
| 3 | 148 | 0.50 | 0.79 | 23 | empty |
| 4 | 104 | 0.46 | 0.79 | 15 | empty |
| 5 | 136 | 0.41 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 761 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 342 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 182 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5C7M · Crystal structure of E3 ligase itch with a ub variant · the same entry in another collection · chain A against A, TM-score 1.00
- Q96J02 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase itchy homolog (Q96J02) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q96J02
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 5C7M · PDBe 5C7M · UniProt Q96J02 · UniProt P0CG48
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