MolNFT v1 · #116007 · protein
Structure of UBE2D2:RNF165:UB complex
5D0K · Ubiquitin-conjugating enzyme E2 D2: “Structure of UBE2D2:RNF165:UB complex”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.67). MolNFT v1 #116007 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5D0K
- Type
- protein
- Length
- 1,169 residues
- Chains
- 12
- 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
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 148 | 37% helix, 21% strand | P62837 |
| C | Ring finger protein 165 | protein | 69 | 22% helix, 22% strand | Q6ZSG1 |
| F, I, L | Ring finger protein 165 | protein | 68 | 19% helix, 22% strand | Q6ZSG1 |
| B, E, H, K | Polyubiquitin-B | protein | 76 | 24% helix, 33% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains C, F, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.67 | 0.78 | 46 | empty |
| 2 | 443 | 0.65 | 0.78 | 52 | empty |
| 3 | 458 | 0.65 | 0.78 | 57 | empty |
| 4 | 519 | 0.65 | 0.76 | 54 | empty |
| 5 | 341 | 0.61 | 0.78 | 59 | empty |
Interfaces
19 interfaces between chains.
- A–G · 985 Ų buried · 17 hydrogen bonds · protein-protein
- F–B · 677 Ų buried · 2 hydrogen bonds · protein-protein
- I–K · 664 Ų buried · 2 hydrogen bonds · protein-protein
- L–H · 619 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 594 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5D0K · Structure of UbE2D2:RNF165:Ub complex · the same entry in another collection · chain K against K, TM-score 1.00
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 5D0K · PDBe 5D0K · UniProt P62837 · UniProt Q6ZSG1 · UniProt P0CG47
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