MolNFT v1 · #137136 · protein
Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin
5VF0 · Polyubiquitin-B: “Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin”. Solution nmr, 1 ligand (ZN), 1 pocket (best druggability 0.32). MolNFT v1 #137136 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5VF0
- Type
- protein
- Length
- 119 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B; E3 ubiquitin-protein ligase RAD18
- EC
- 2.3.2.27
- UniProt
- P0CG47, Q9NS91
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.32
Structure
solution nmr · 2 distinct chains · 25% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyubiquitin-B | protein | 76 | 20% helix, 34% strand | P0CG47 |
| B | E3 ubiquitin-protein ligase RAD18 (EC 2.3.2.27) | protein | 43 | 35% helix, 9% strand | Q9NS91 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 468 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VF0 · Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NS91 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RAD18 (Q9NS91) · a predicted model of the same protein · chain B against A, TM-score 0.61
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 P0CG47
- Every structure of UniProt Q9NS91
- Elsewhere: RCSB PDB 5VF0 · PDBe 5VF0 · UniProt P0CG47 · UniProt Q9NS91
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