MolNFT v1 · #122120 · protein
Structure of the stable UBE2D3-ubdha conjugate
5IFR · Ubiquitin-conjugating enzyme E2 D3: “Structure of the stable UBE2D3-ubdha conjugate”. X-ray diffraction, 1 pocket (best druggability 0.54). MolNFT v1 #122120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IFR
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D3; Polyubiquitin-B
- EC
- 2.3.2.23, 2.3.2.24
- UniProt
- P61077, P0CG47
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D3 (EC 2.3.2.23, 2.3.2.24) | protein | 151 | 38% helix, 18% strand | P61077 |
| B | Polyubiquitin-B | protein | 76 | 20% helix, 33% strand | P0CG47 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.54 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 P61077
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5IFR · PDBe 5IFR · UniProt P61077 · UniProt P0CG47
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