MolNFT v1 · #139537 · protein
Crystal structure of RNF168 UDM1 in complex with LYS63-linked diubiquitin, form I
5XIS: “Crystal structure of RNF168 UDM1 in complex with LYS63-linked diubiquitin, form I”. X-ray diffraction, 2 ligands (XYZ, MG). MolNFT v1 #139537 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XIS
- Type
- protein
- Length
- 458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q8IYW5, P62983
- Ligands
- XYZ, MG
Structure
x-ray diffraction · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 79 | — | Q8IYW5 |
| B | — | protein | 72 | — | P62983 |
| C, F | — | protein | 76 | — | P62983 |
| D | — | protein | 82 | — | Q8IYW5 |
| E | — | protein | 73 | — | P62983 |
Ligands and binding sites
- XYZ · beta-D-xylofuranose · ligand · 2 copies · chains A, B, D
- MG · Magnesium ion · metal · 2 copies · chains B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5XIS · Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I · the same entry in another collection · chain F against F, 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 0.99
- 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 0.88
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 5XIS · PDBe 5XIS · UniProt Q8IYW5 · UniProt P62983
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