MolNFT v2 · #175723 · protein
Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.
7B5N · Cullin-1: “Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly…”. Electron microscopy at 3.6, 2 ligands (SY8, ZN), 16 pockets (best druggability 0.81). MolNFT v2 #175723 on GenesisL1: 3D structure, binding…
- PDB
- 7B5N
- Type
- protein
- Length
- 1,229 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Homo sapiens
- Molecule
- Cullin-1; E3 ubiquitin-protein ligase ARIH1; Polyubiquitin-C; NEDD8; E3 ubiquitin-protein…
- EC
- 2.3.2.31, 2.3.2.27, 2.3.2.32, 2.3.2.23
- UniProt
- Q13616, Q9Y4X5, P0CG48, Q15843, P62877, P68036
- Ligands
- SY8, ZN
- Pockets
- 16 · best druggability 0.81
Structure
electron microscopy · resolution 3.6 · 6 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cullin-1 | protein | 423 | 55% helix, 8% strand | Q13616 |
| H | E3 ubiquitin-protein ligase ARIH1 (EC 2.3.2.31) | protein | 423 | 54% helix, 6% strand | Q9Y4X5 |
| U | Polyubiquitin-C | protein | 75 | 15% helix, 37% strand | P0CG48 |
| N | NEDD8 | protein | 76 | 16% helix, 28% strand | Q15843 |
| R | E3 ubiquitin-protein ligase RBX1 (EC 2.3.2.27, 2.3.2.32) | protein | 81 | 12% helix, 21% strand | P62877 |
| D | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 151 | 35% helix, 15% strand | P68036 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.81 | 0.85 | 94 | empty |
| 2 | 648 | 0.73 | 0.79 | 53 | empty |
| 3 | 588 | 0.65 | 0.76 | 63 | empty |
| 4 | 76 | 0.60 | 0.89 | 14 | empty |
| 5 | 378 | 0.60 | 0.76 | 43 | empty |
Interfaces
7 interfaces between chains.
- C–R · 1828 Ų buried · 28 hydrogen bonds · protein-protein
- H–U · 1335 Ų buried · 11 hydrogen bonds · protein-protein
- H–D · 959 Ų buried · 8 hydrogen bonds · protein-protein
- C–H · 793 Ų buried · 3 hydrogen bonds · protein-protein
- H–R · 625 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7B5N · Ubiquitin ligation to F-box protein substrates by scf-rbr E3-E3 super- assembly… · the same entry in another collection · chain U against U, TM-score 1.00
- P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P0CG48 · AlphaFold monomer V2.0 prediction for polyubiquitin-C (P0CG48) · a predicted model of the same protein · chain U against A, TM-score 0.90
- Q15843 · AlphaFold monomer V2.0 prediction for NEDD8 (Q15843) · a predicted model of the same protein · chain N against A, TM-score 0.90
- Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain C against A, TM-score 0.79
- P62877 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RBX1 (P62877) · a predicted model of the same protein · chain R against A, TM-score 0.76
- Q9Y4X5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ARIH1 (Q9Y4X5) · a predicted model of the same protein · chain H against A, TM-score 0.58
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 Q13616
- Every structure of UniProt Q9Y4X5
- Every structure of UniProt P0CG48
- Every structure of UniProt Q15843
- Every structure of UniProt P62877
- Every structure of UniProt P68036
- Elsewhere: RCSB PDB 7B5N · PDBe 7B5N · UniProt Q13616 · UniProt Q9Y4X5 · UniProt P0CG48 · UniProt Q15843 · UniProt P62877 · UniProt P68036
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