MolNFT v1 · #136934 · protein
Structure of DCN4 pony domain bound to CUL1 whb
5V89 · DCN1-like protein 4: “Structure of DCN4 pony domain bound to CUL1 whb”. X-ray diffraction, 3 pockets (best druggability 0.54). MolNFT v1 #136934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5V89
- Type
- protein
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DCN1-like protein 4; Cullin-1
- UniProt
- Q92564, Q13616
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DCN1-like protein 4 | protein | 190 | 62% helix, 5% strand | Q92564 |
| C | Cullin-1 | protein | 67 | 64% helix, 15% strand | Q13616 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.54 | 0.82 | 21 | empty |
| 2 | 254 | 0.51 | 0.75 | 32 | empty |
| 3 | 52 | 0.31 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 530 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5V89 · Structure of DCN4 PONY domain bound to CUL1 WHB · the same entry in another collection · chain A against A, TM-score 1.00
- Q92564 · AlphaFold monomer V2.0 prediction for DCN1-like protein 4 (Q92564) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q92564
- Every structure of UniProt Q13616
- Elsewhere: RCSB PDB 5V89 · PDBe 5V89 · UniProt Q92564 · UniProt Q13616
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