MolNFT v1 · #123814 · protein
Crystal structure of sopa-TRIM56 complex
5JW7 · E3 ubiquitin-protein ligase sopa: “Crystal structure of sopa-TRIM56 complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.51). MolNFT v1 #123814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JW7
- Type
- protein
- Length
- 323 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase sopa; E3 ubiquitin-protein ligase TRIM56
- EC
- 6.3.2.-
- UniProt
- Q8ZNR3, Q9BRZ2
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase sopa (EC 6.3.2.-) | protein | 262 | 33% helix, 13% strand | Q8ZNR3 |
| B | E3 ubiquitin-protein ligase TRIM56 (EC 6.3.2.-) | protein | 61 | 11% helix, 13% strand | Q9BRZ2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.51 | 0.79 | 29 | empty |
| 2 | 83 | 0.50 | 0.83 | 19 | empty |
| 3 | 56 | 0.31 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5JW7 · Crystal structure of SopA-Trim56 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZNR3 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase sopa (Q8ZNR3) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9BRZ2 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM56 (Q9BRZ2) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q8ZNR3
- Every structure of UniProt Q9BRZ2
- Elsewhere: RCSB PDB 5JW7 · PDBe 5JW7 · UniProt Q8ZNR3 · UniProt Q9BRZ2
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