Research workbench
Structure of a glomulin-RBX1-CUL1 complex
Analyse Structure of a glomulin-RBX1-CUL1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F52
- Type
- protein
- Length
- 1,716 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-1; E3 ubiquitin-protein ligase RBX1; Glomulin
- EC
- 6.3.2.-
- UniProt
- Q13616, P62877, Q92990
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cullin-1 | protein | 258 | 51% helix, 16% strand | Q13616 |
| B | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 84 | 13% helix, 31% strand | P62877 |
| C | Cullin-1 | protein | 254 | 48% helix, 15% strand | Q13616 |
| D | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 85 | 18% helix, 29% strand | P62877 |
| E | Glomulin | protein | 523 | 73% helix, 0% strand | Q92990 |
| F | Glomulin | protein | 512 | 71% helix, 0% strand | Q92990 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.83 | 0.84 | 105 | empty |
| 2 | 697 | 0.77 | 0.82 | 55 | empty |
| 3 | 539 | 0.69 | 0.79 | 52 | empty |
| 4 | 364 | 0.65 | 0.80 | 43 | empty |
| 5 | 457 | 0.65 | 0.77 | 47 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1758 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1731 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 1235 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1213 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1181 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4F52 · Structure of a Glomulin-RBX1-CUL1 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q92990 · AlphaFold monomer V2.0 prediction for glomulin (Q92990) · a predicted model of the same protein · chain E against A, TM-score 0.96
- Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P62877 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RBX1 (P62877) · a predicted model of the same protein · chain B against A, TM-score 0.72
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 P62877
- Every structure of UniProt Q92990
- Elsewhere: RCSB PDB 4F52 · PDBe 4F52 · UniProt Q13616 · UniProt P62877 · UniProt Q92990
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