MolNFT v1 · #92539 · protein
Dcnl complex with N-terminally acetylated NEDD8 E2 peptide
4GBA · DCN1-like protein 3: “Dcnl complex with N-terminally acetylated NEDD8 E2 peptide”. X-ray diffraction, 4 pockets (best druggability 0.60). MolNFT v1 #92539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GBA
- Type
- protein
- Length
- 420 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DCN1-like protein 3; NEDD8-conjugating enzyme UBE2F
- UniProt
- Q8IWE4, Q969M7
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DCN1-like protein 3 | protein | 196 | 59% helix, 4% strand | Q8IWE4 |
| B | DCN1-like protein 3 | protein | 206 | 60% helix, 5% strand | Q8IWE4 |
| F, G | NEDD8-conjugating enzyme UBE2F | protein | 9 | 56% helix, 0% strand | Q969M7 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.60 | 0.76 | 49 | empty |
| 2 | 68 | 0.41 | 0.80 | 18 | empty |
| 3 | 102 | 0.37 | 0.75 | 24 | empty |
| 4 | 59 | 0.26 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 724 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 565 Ų buried · 1 hydrogen bond · protein-protein
- B–G · 535 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4GBA · DCNL complex with N-terminally acetylated NEDD8 E2 peptide · the same entry in another collection · chain B against B, TM-score 1.00
- Q8IWE4 · AlphaFold monomer V2.0 prediction for DCN1-like protein 3 (Q8IWE4) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q969M7 · AlphaFold monomer V2.0 prediction for NEDD8-conjugating enzyme UBE2F (Q969M7) · a predicted model of the same protein · chain F against A, TM-score 0.70
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 Q8IWE4
- Every structure of UniProt Q969M7
- Elsewhere: RCSB PDB 4GBA · PDBe 4GBA · UniProt Q8IWE4 · UniProt Q969M7
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