MolNFT v1 · #73462 · protein
A dual E3 mechanism for RUB1 ligation to CDC53: DCN1(P)-CDC53(WHB)
3O2P · Defective in cullin neddylation protein 1: “A dual E3 mechanism for RUB1 ligation to CDC53: DCN1(P)-CDC53(WHB)”. X-ray diffraction, 1 pocket (best druggability 0.52). MolNFT v1 #73462 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3O2P
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Defective in cullin neddylation protein 1; Cell division control protein 53
- UniProt
- Q12395, Q12018
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Defective in cullin neddylation protein 1 | protein | 199 | 64% helix, 4% strand | Q12395 |
| E | Cell division control protein 53 | protein | 86 | 62% helix, 12% strand | Q12018 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.52 | 0.75 | 38 | empty |
Interfaces
1 interface between chains.
- A–E · 490 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3O2P · A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) · the same entry in another collection · chain A against A, TM-score 1.00
- Q12395 · AlphaFold monomer V2.0 prediction for defective in cullin neddylation protein 1 (Q12395) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q12018 · AlphaFold monomer V2.0 prediction for cell division control protein 53 (Q12018) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 Q12395
- Every structure of UniProt Q12018
- Elsewhere: RCSB PDB 3O2P · PDBe 3O2P · UniProt Q12395 · UniProt Q12018
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