MolNFT v1 · #134715 · protein
Crystal structure of the human ubr-box domain from UBR2 in complex with asymmetrically double methylated arginine peptide
5TDB · E3 ubiquitin-protein ligase UBR2: “Crystal structure of the human ubr-box domain from UBR2 in complex with asymmetrically double methylated…”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #134715 on GenesisL1: 3D structure, binding…
- PDB
- 5TDB
- Type
- protein
- Length
- 72 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UBR2; DA2-ile-phe-ser peptide
- EC
- 6.3.2.-
- UniProt
- Q8IWV8
- Ligands
- ZN
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UBR2 (EC 6.3.2.-) | protein | 70 | 13% helix, 21% strand | Q8IWV8 |
| B | DA2-ile-phe-ser peptide | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 315 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5TDB · Crystal structure of the human UBR-box domain from UBR2 in complex with asymmetrically… · 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 0.97
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 Q8IWV8
- Elsewhere: RCSB PDB 5TDB · PDBe 5TDB · UniProt Q8IWV8
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