MolNFT v1 · #173622 · protein
Ubiquitin ligation to F-box protein substrates by scf-rbr E3-E3 super- assembly: CUL1-RBX1-ARIH1 ariadne. transition state 1
7B5S · Cullin-1: “Ubiquitin ligation to F-box protein substrates by scf-rbr E3-E3 super- assembly: CUL1-RBX1-ARIH1 ariadne.…”. Electron microscopy, 1 ligand (ZN), 12 pockets (best druggability 0.66). MolNFT v1 #173622 on GenesisL1: 3D…
- PDB
- 7B5S
- Type
- protein
- Length
- 931 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-1; E3 ubiquitin-protein ligase ARIH1; E3 ubiquitin-protein ligase RBX1
- EC
- 2.3.2.31, 2.3.2.27, 2.3.2.32
- UniProt
- Q13616, Q9Y4X5, P62877
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.66
Structure
electron microscopy · 3 distinct chains · 58% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cullin-1 | protein | 634 | 61% helix, 5% strand | Q13616 |
| H | E3 ubiquitin-protein ligase ARIH1 (EC 2.3.2.31) | protein | 216 | 62% helix, 8% strand | Q9Y4X5 |
| R | E3 ubiquitin-protein ligase RBX1 (EC 2.3.2.27, 2.3.2.32) | protein | 81 | 17% helix, 19% strand | P62877 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains H, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.66 | 0.76 | 66 | empty |
| 2 | 341 | 0.57 | 0.76 | 40 | empty |
| 3 | 76 | 0.55 | 0.86 | 18 | empty |
| 4 | 74 | 0.51 | 0.85 | 17 | empty |
| 5 | 219 | 0.51 | 0.76 | 35 | empty |
Interfaces
3 interfaces between chains.
- C–R · 1802 Ų buried · 25 hydrogen bonds · protein-protein
- H–R · 651 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 476 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7B5S · Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly… · the same entry in another collection · chain C against C, TM-score 1.00
- Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain C against A, TM-score 0.94
- 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 0.87
- 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
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 P62877
- Elsewhere: RCSB PDB 7B5S · PDBe 7B5S · UniProt Q13616 · UniProt Q9Y4X5 · UniProt P62877
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