Research workbench
Crystal structure of rbr E3 ligase RNF216 with ubiquitin
Analyse Crystal structure of rbr E3 ligase RNF216 with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M4M
- Type
- protein
- Length
- 493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF216; Ubiquitin
- EC
- 2.3.2.27
- UniProt
- Q9NWF9, P0CG48
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF216 (EC 2.3.2.27) | protein | 173 | 31% helix, 19% strand | Q9NWF9 |
| B | E3 ubiquitin-protein ligase RNF216 (EC 2.3.2.27) | protein | 168 | 32% helix, 18% strand | Q9NWF9 |
| C, D | Ubiquitin | protein | 76 | 20% helix, 32% strand | P0CG48 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.50 | 0.79 | 25 | empty |
| 2 | 131 | 0.45 | 0.77 | 25 | empty |
| 3 | 111 | 0.41 | 0.76 | 26 | GOL |
| 4 | 62 | 0.35 | 0.78 | 18 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 1267 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1263 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 205 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7M4M · Crystal structure of RBR E3 ligase RNF216 with ubiquitin · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NWF9 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF216 (Q9NWF9) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 Q9NWF9
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 7M4M · PDBe 7M4M · UniProt Q9NWF9 · UniProt P0CG48
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