MolNFT v1 · #38412 · protein
Structure of a USP8-NRDP1 complex
2GWF · Ubiquitin carboxyl-terminal hydrolase 8: “Structure of a USP8-NRDP1 complex”. X-ray diffraction, 8 pockets (best druggability 0.85). MolNFT v1 #38412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GWF
- Type
- protein
- Length
- 776 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 8; Ring finger protein 41
- EC
- 3.1.2.15, 6.3.2.-
- UniProt
- P40818, Q9H4P4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) | protein | 136 | 41% helix, 14% strand | P40818 |
| B | Ring finger protein 41 (EC 6.3.2.-) | protein | 121 | 44% helix, 18% strand | Q9H4P4 |
| C | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) | protein | 134 | 41% helix, 14% strand | P40818 |
| D | Ring finger protein 41 (EC 6.3.2.-) | protein | 126 | 43% helix, 17% strand | Q9H4P4 |
| E | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) | protein | 137 | 41% helix, 14% strand | P40818 |
| F | Ring finger protein 41 (EC 6.3.2.-) | protein | 122 | 43% helix, 19% strand | Q9H4P4 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.85 | 0.87 | 105 | empty |
| 2 | 403 | 0.64 | 0.78 | 33 | empty |
| 3 | 147 | 0.63 | 0.86 | 25 | empty |
| 4 | 303 | 0.58 | 0.77 | 47 | empty |
| 5 | 146 | 0.52 | 0.80 | 26 | empty |
Interfaces
11 interfaces between chains.
- E–F · 519 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 504 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 501 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 493 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 422 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2GWF · Structure of a USP8-NRDP1 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q9H4P4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase NRDP1 (Q9H4P4) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P40818 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 8 (P40818) · 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 P40818
- Every structure of UniProt Q9H4P4
- Elsewhere: RCSB PDB 2GWF · PDBe 2GWF · UniProt P40818 · UniProt Q9H4P4
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