MolNFT v1 · #173616 · protein
Ubiquitin ligation to F-box protein substrates by scf-rbr E3-E3 super- assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~UB~ARIH1. transition state 2
7B5M · Cullin-1: “Ubiquitin ligation to F-box protein substrates by scf-rbr E3-E3 super- assembly…”. Electron microscopy, 2 ligands (DHA, ZN), 20 pockets (best druggability 0.80). MolNFT v1 #173616 on GenesisL1: 3D structure, binding sites…
- PDB
- 7B5M
- Type
- protein
- Length
- 1,560 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-1; E3 ubiquitin-protein ligase ARIH1; S-phase kinase-associated protein 2…
- EC
- 2.3.2.31, 2.3.2.27, 2.3.2.32
- UniProt
- Q13616, Q9Y4X5, Q13309, P61024, P63208, P0CG48, P62877, P46527
- Ligands
- DHA, ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 8 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cullin-1 | protein | 634 | 62% helix, 4% strand | Q13616 |
| H | E3 ubiquitin-protein ligase ARIH1 (EC 2.3.2.31) | protein | 226 | 64% helix, 1% strand | Q9Y4X5 |
| T | S-phase kinase-associated protein 2 | protein | 325 | 30% helix, 13% strand | Q13309 |
| K | Cyclin-dependent kinases regulatory subunit 1 | protein | 69 | 16% helix, 28% strand | P61024 |
| S | S-phase kinase-associated protein 1 | protein | 140 | 47% helix, 7% strand | P63208 |
| U | Polyubiquitin-C | protein | 75 | 16% helix, 23% strand | P0CG48 |
| R | E3 ubiquitin-protein ligase RBX1 (EC 2.3.2.27, 2.3.2.32) | protein | 81 | 14% helix, 22% strand | P62877 |
| P | Cyclin-dependent kinase inhibitor 1B | protein | 10 | 0% helix, 0% strand | P46527 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.80 | 0.97 | 27 | empty |
| 2 | 59 | 0.73 | 0.98 | 16 | empty |
| 3 | 483 | 0.73 | 0.82 | 69 | empty |
| 4 | 415 | 0.65 | 0.78 | 44 | empty |
| 5 | 178 | 0.63 | 0.84 | 33 | empty |
Interfaces
10 interfaces between chains.
- C–R · 1789 Ų buried · 31 hydrogen bonds · protein-protein
- T–S · 1368 Ų buried · 8 hydrogen bonds · protein-protein
- H–U · 1077 Ų buried · 5 hydrogen bonds · protein-protein
- T–K · 941 Ų buried · 11 hydrogen bonds · protein-protein
- C–S · 746 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 7B5M · Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly… · the same entry in another collection · chain P against P, TM-score 1.00
- Q13309 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 2 (Q13309) · a predicted model of the same protein · chain T against A, TM-score 0.97
- Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain S against A, TM-score 0.93
- P0CG48 · AlphaFold monomer V2.0 prediction for polyubiquitin-C (P0CG48) · a predicted model of the same protein · chain U against A, TM-score 0.88
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 Q13309
- Every structure of UniProt P61024
- Every structure of UniProt P63208
- Every structure of UniProt P0CG48
- Every structure of UniProt P62877
- Every structure of UniProt P46527
- Elsewhere: RCSB PDB 7B5M · PDBe 7B5M · UniProt Q13616 · UniProt Q9Y4X5 · UniProt Q13309 · UniProt P61024 · UniProt P63208 · UniProt P0CG48 · UniProt P62877 · UniProt P46527
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