Research workbench
Crystal structure of an rbr E3 ubiquitin ligase in complex with an E2- ub thioester intermediate mimic
Analyse Crystal structure of an rbr E3 ubiquitin ligase in complex with an E2- ub… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TTE
- Type
- protein
- Length
- 672 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase ARIH1; Ubiquitin-conjugating enzyme E2 L3; Ubiquitin
- EC
- 2.3.2.-, 2.3.2.23
- UniProt
- Q9Y4X5, P68036, A0A1D6DHW0
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | E3 ubiquitin-protein ligase ARIH1 (EC 2.3.2.-) | protein | 442 | 49% helix, 10% strand | Q9Y4X5 |
| E | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 151 | 34% helix, 17% strand | P68036 |
| F | Ubiquitin | protein | 79 | 19% helix, 34% strand | A0A1D6DHW0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.72 | 0.78 | 72 | empty |
| 2 | 84 | 0.58 | 0.88 | 19 | empty |
| 3 | 248 | 0.55 | 0.77 | 29 | empty |
| 4 | 60 | 0.53 | 0.87 | 14 | empty |
| 5 | 63 | 0.46 | 0.83 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–E · 802 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 707 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 235 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5TTE · Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester… · the same entry in another collection · chain B against B, TM-score 1.00
- P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain E against A, TM-score 0.98
- Q9Y4X5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ARIH1 (Q9Y4X5) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9Y4X5
- Every structure of UniProt P68036
- Every structure of UniProt A0A1D6DHW0
- Elsewhere: RCSB PDB 5TTE · PDBe 5TTE · UniProt Q9Y4X5 · UniProt P68036 · UniProt A0A1D6DHW0
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