MolNFT v1 · #27758 · protein
Crystal structure of DEN1 in complex with NEDD8
1XT9 · Sentrin-specific protease 8: “Crystal structure of DEN1 in complex with NEDD8”. X-ray diffraction, 2 pockets (best druggability 0.47). MolNFT v1 #27758 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XT9
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sentrin-specific protease 8; Neddylin
- EC
- 3.4.22.-
- UniProt
- Q96LD8, Q15843
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sentrin-specific protease 8 (EC 3.4.22.-) | protein | 208 | 44% helix, 19% strand | Q96LD8 |
| B | Neddylin | protein | 76 | 20% helix, 38% strand | Q15843 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.47 | 0.78 | 26 | empty |
| 2 | 64 | 0.35 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1584 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1XT9 · Crystal Structure of Den1 in complex with Nedd8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q96LD8 · AlphaFold monomer V2.0 prediction for sentrin-specific protease 8 (Q96LD8) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q15843 · AlphaFold monomer V2.0 prediction for NEDD8 (Q15843) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q96LD8
- Every structure of UniProt Q15843
- Elsewhere: RCSB PDB 1XT9 · PDBe 1XT9 · UniProt Q96LD8 · UniProt Q15843
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