Research workbench
A dual E3 mechanism for RUB1 ligation to CDC53: DCN1(P)-CDC53(WHB) low resolution
Analyse A dual E3 mechanism for RUB1 ligation to CDC53: DCN1(P)-CDC53(WHB) low… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O6B
- Type
- protein
- Length
- 1,272 residues
- Chains
- 10
- 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
- 16 · best druggability 0.70
Structure
x-ray diffraction · 10 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Defective in cullin neddylation protein 1 | protein | 195 | 65% helix, 4% strand | Q12395 |
| B | Cell division control protein 53 | protein | 70 | 54% helix, 13% strand | Q12018 |
| C | Defective in cullin neddylation protein 1 | protein | 198 | 61% helix, 4% strand | Q12395 |
| D | Cell division control protein 53 | protein | 68 | 56% helix, 13% strand | Q12018 |
| E | Defective in cullin neddylation protein 1 | protein | 195 | 63% helix, 4% strand | Q12395 |
| F | Cell division control protein 53 | protein | 68 | 57% helix, 15% strand | Q12018 |
| G | Defective in cullin neddylation protein 1 | protein | 192 | 62% helix, 4% strand | Q12395 |
| H | Cell division control protein 53 | protein | 68 | 50% helix, 15% strand | Q12018 |
| I | Defective in cullin neddylation protein 1 | protein | 157 | 54% helix, 3% strand | Q12395 |
| J | Cell division control protein 53 | protein | 61 | 51% helix, 13% strand | Q12018 |
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.70 | 0.78 | 66 | empty |
| 2 | 311 | 0.60 | 0.78 | 44 | empty |
| 3 | 321 | 0.58 | 0.77 | 24 | empty |
| 4 | 237 | 0.55 | 0.78 | 35 | empty |
| 5 | 250 | 0.55 | 0.77 | 39 | empty |
Interfaces
13 interfaces between chains.
- E–F · 649 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 610 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 576 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 567 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 526 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3O6B · A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) low resolution · the same entry in another collection · chain J against J, 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 C 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 Q12395
- Every structure of UniProt Q12018
- Elsewhere: RCSB PDB 3O6B · PDBe 3O6B · UniProt Q12395 · UniProt Q12018
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