Research workbench
Crystal structure of the human ubr-box domain from UBR1 in complex with monomethylated arginine peptide.
Analyse Crystal structure of the human ubr-box domain from UBR1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TDC
- Type
- protein
- Length
- 148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UBR1; Nmm-ile-phe-ser peptide
- EC
- 6.3.2.-
- UniProt
- Q8IWV7
- Ligands
- ZN, SO4
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UBR1 (EC 6.3.2.-) | protein | 70 | 13% helix, 23% strand | Q8IWV7 |
| C | E3 ubiquitin-protein ligase UBR1 (EC 6.3.2.-) | protein | 71 | 13% helix, 21% strand | Q8IWV7 |
| B | Nmm-ile-phe-ser peptide | protein | 3 | 0% helix, 0% strand | — |
| D | Nmm-ile-phe-ser peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–C · 471 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 360 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 336 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5TDC · Crystal structure of the human UBR-box domain from UBR1 in complex with monomethylated… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IWV7 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UBR1 (Q8IWV7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8IWV7
- Elsewhere: RCSB PDB 5TDC · PDBe 5TDC · UniProt Q8IWV7
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