Research workbench
Structure of the ubr-box of UBR2 ubiquitin ligase
Analyse Structure of the ubr-box of UBR2 ubiquitin ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NY2
- Type
- protein
- Length
- 575 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UBR2
- EC
- 6.3.2.-
- UniProt
- Q8IWV8
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, H | E3 ubiquitin-protein ligase UBR2 (EC 6.3.2.-) | protein | 72 | 11% helix, 21% strand | Q8IWV8 |
| C | E3 ubiquitin-protein ligase UBR2 (EC 6.3.2.-) | protein | 71 | 17% helix, 21% strand | Q8IWV8 |
| D, G | E3 ubiquitin-protein ligase UBR2 (EC 6.3.2.-) | protein | 73 | 16% helix, 21% strand | Q8IWV8 |
| E | E3 ubiquitin-protein ligase UBR2 (EC 6.3.2.-) | protein | 70 | 17% helix, 21% strand | Q8IWV8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.71 | 0.78 | 80 | empty |
| 2 | 288 | 0.67 | 0.83 | 37 | empty |
| 3 | 302 | 0.52 | 0.74 | 47 | empty |
| 4 | 153 | 0.49 | 0.78 | 24 | empty |
| 5 | 99 | 0.35 | 0.74 | 24 | empty |
Interfaces
10 interfaces between chains.
- A–H · 532 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 500 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 489 Ų buried · 15 hydrogen bonds · protein-protein
- B–H · 396 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 346 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 Q8IWV8
- Elsewhere: RCSB PDB 3NY2 · PDBe 3NY2 · UniProt Q8IWV8
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