MolNFT v1 · #139539 · protein
Crystal structure of RNF168 UDM2 in complex with LYS63-linked diubiquitin
5XIU · E3 ubiquitin-protein ligase RNF168: “Crystal structure of RNF168 UDM2 in complex with LYS63-linked diubiquitin”. X-ray diffraction. MolNFT v1 #139539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XIU
- Type
- protein
- Length
- 120 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF168; Ubiquitin-40S ribosomal protein S27A
- EC
- 2.3.2.27
- UniProt
- Q8IYW5, P62983
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF168 (EC 2.3.2.27) | protein | 47 | 79% helix, 0% strand | Q8IYW5 |
| B | Ubiquitin-40S ribosomal protein S27A | protein | 73 | 25% helix, 34% strand | P62983 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 840 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5XIU · Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P62983 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62983) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q8IYW5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF168 (Q8IYW5) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 Q8IYW5
- Every structure of UniProt P62983
- Elsewhere: RCSB PDB 5XIU · PDBe 5XIU · UniProt Q8IYW5 · UniProt P62983
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