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Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold Protein Complex
Analyse Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold Protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X57
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Arabidopsis thaliana
- Molecule
- Ubiquitin-conjugating enzyme E2 8; Membrane-anchored ubiquitin-fold protein 3
- EC
- 6.3.2.19
- UniProt
- P35131, Q9SW27
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · resolution 2.8 · 4 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 8 (EC 6.3.2.19) | protein | 148 | 37% helix, 18% strand | P35131 |
| B | Membrane-anchored ubiquitin-fold protein 3 | protein | 93 | 18% helix, 34% strand | Q9SW27 |
| C | Ubiquitin-conjugating enzyme E2 8 (EC 6.3.2.19) | protein | 149 | 37% helix, 18% strand | P35131 |
| D | Membrane-anchored ubiquitin-fold protein 3 | protein | 92 | 12% helix, 35% strand | Q9SW27 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.55 | 0.88 | 20 | SO4 |
| 2 | 127 | 0.52 | 0.81 | 20 | empty |
| 3 | 73 | 0.51 | 0.85 | 22 | empty |
| 4 | 127 | 0.50 | 0.80 | 23 | empty |
| 5 | 73 | 0.47 | 0.83 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 958 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 945 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 424 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4X57 · Structure of an arabidopsis E2 / membrane-anchored ubiquitin-fold protein complex · the same entry in another collection · chain D against D, TM-score 1.00
- P35131 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 8 (P35131) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9SW27 · AlphaFold monomer V2.0 prediction for membrane-anchored ubiquitin- fold protein 3 (Q9SW27) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 P35131
- Every structure of UniProt Q9SW27
- Elsewhere: RCSB PDB 4X57 · PDBe 4X57 · UniProt P35131 · UniProt Q9SW27
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