MolNFT v1 · #116008 · protein
Structure of UBE2D2:RNF165:UB complex
5D0M · Ubiquitin-conjugating enzyme E2 D2: “Structure of UBE2D2:RNF165:UB complex”. X-ray diffraction, 2 ligands (ZN, PO4), 3 pockets (best druggability 0.68). MolNFT v1 #116008 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5D0M
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; Ring finger protein 165; Polyubiquitin-B
- EC
- 6.3.2.19
- UniProt
- P62837, Q6ZSG1, P0CG47
- Ligands
- ZN, PO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 147 | 37% helix, 21% strand | P62837 |
| C | Ring finger protein 165 | protein | 60 | 22% helix, 25% strand | Q6ZSG1 |
| B | Polyubiquitin-B | protein | 76 | 20% helix, 33% strand | P0CG47 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.68 | 0.83 | 40 | PO4 |
| 2 | 69 | 0.31 | 0.74 | 13 | empty |
| 3 | 59 | 0.25 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 693 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 161 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5D0M · Structure of UbE2D2:RNF165:Ub complex · the same entry in another collection · chain A against A, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q6ZSG1 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF165 (Q6ZSG1) · a predicted model of the same protein · chain C 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 P62837
- Every structure of UniProt Q6ZSG1
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5D0M · PDBe 5D0M · UniProt P62837 · UniProt Q6ZSG1 · UniProt P0CG47
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