Research workbench
Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1
Analyse Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B5L
- Type
- protein
- Length
- 2,654 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Homo sapiens
- 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, 2.3.2.23, 2.7.11.22
- UniProt
- Q13616, Q9Y4X5, Q13309, P61024, P63208, P0CG48, Q15843, P62877, P68036, P24941, P20248, P46527
- Ligands
- SY8, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.8 · 12 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cullin-1 | protein | 706 | 62% helix, 5% strand | Q13616 |
| H | E3 ubiquitin-protein ligase ARIH1 (EC 2.3.2.31) | protein | 423 | 53% helix, 8% strand | Q9Y4X5 |
| T | S-phase kinase-associated protein 2 | protein | 321 | 31% helix, 9% strand | Q13309 |
| K | Cyclin-dependent kinases regulatory subunit 1 | protein | 69 | 16% helix, 33% strand | P61024 |
| S | S-phase kinase-associated protein 1 | protein | 138 | 53% helix, 8% strand | P63208 |
| U | Polyubiquitin-C | protein | 75 | 20% helix, 37% strand | P0CG48 |
| N | NEDD8 | protein | 76 | 16% helix, 32% strand | Q15843 |
| R | E3 ubiquitin-protein ligase RBX1 (EC 2.3.2.27, 2.3.2.32) | protein | 81 | 12% helix, 26% strand | P62877 |
| D | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 151 | 34% helix, 16% strand | P68036 |
| L | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 284 | 33% helix, 11% strand | P24941 |
| Y | Cyclin-A2 | protein | 253 | 69% helix, 0% strand | P20248 |
| P | Cyclin-dependent kinase inhibitor 1B | protein | 77 | 29% helix, 5% 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.82 | 0.93 | 40 | empty |
| 2 | 442 | 0.75 | 0.84 | 58 | empty |
| 3 | 681 | 0.72 | 0.79 | 79 | empty |
| 4 | 621 | 0.72 | 0.79 | 74 | empty |
| 5 | 644 | 0.72 | 0.79 | 50 | empty |
Interfaces
18 interfaces between chains.
- C–R · 1820 Ų buried · 28 hydrogen bonds · protein-protein
- L–P · 1656 Ų buried · 18 hydrogen bonds · protein-protein
- L–Y · 1517 Ų buried · 16 hydrogen bonds · protein-protein
- T–S · 1474 Ų buried · 8 hydrogen bonds · protein-protein
- H–U · 1290 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 2 modified, 1 isopeptide (covalent ligand, phosphorylation, isopeptide).
Compared structures
- 7B5L · Ubiquitin ligation to F-box protein substrates by scf-rbr E3-E3 super- assembly… · the same entry in another collection · chain Y against Y, TM-score 1.00
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 Q15843
- Every structure of UniProt P62877
- Every structure of UniProt P68036
- Every structure of UniProt P24941
- Every structure of UniProt P20248
- Every structure of UniProt P46527
- Elsewhere: RCSB PDB 7B5L · PDBe 7B5L · UniProt Q13616 · UniProt Q9Y4X5 · UniProt Q13309 · UniProt P61024 · UniProt P63208 · UniProt P0CG48 · UniProt Q15843 · UniProt P62877 · UniProt P68036 · UniProt P24941 · UniProt P20248 · UniProt P46527
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