MolNFT v1 · #134714 · protein
Crystal structure of the ubr-box domain from UBR2 in complex with rlws N-degron
5TDA · E3 ubiquitin-protein ligase UBR2: “Crystal structure of the ubr-box domain from UBR2 in complex with rlws N-degron”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #134714 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5TDA
- Type
- protein
- Length
- 75 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UBR2; Arg-leu-TRP-ser peptide
- EC
- 6.3.2.-
- UniProt
- Q8IWV8
- Ligands
- ZN
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UBR2 (EC 6.3.2.-) | protein | 71 | 13% helix, 23% strand | Q8IWV8 |
| B | Arg-leu-TRP-ser peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 322 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5TDA · Crystal structure of the UBR-box domain from UBR2 in complex with RLWS N-degron · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IWV8 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UBR2 (Q8IWV8) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 5TDA · PDBe 5TDA · UniProt Q8IWV8
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