MolNFT v1 · #32921 · protein
Crystal structure of human ubiquitin-conjugating enzyme UBCH5A
2C4P · Ubiquitin-conjugating enzyme E2 D1: “Crystal structure of human ubiquitin-conjugating enzyme UBCH5A”. X-ray diffraction, 3 pockets (best druggability 0.58). MolNFT v1 #32921 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2C4P
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D1
- EC
- 6.3.2.19
- UniProt
- P51668
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 150 | 34% helix, 20% strand | P51668 |
| B | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 149 | 36% helix, 17% strand | P51668 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.58 | 0.77 | 30 | empty |
| 2 | 212 | 0.55 | 0.79 | 27 | empty |
| 3 | 70 | 0.48 | 0.83 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2C4P · Crystal structure of human ubiquitin-conjugating enzyme UbcH5A · the same entry in another collection · chain A against A, TM-score 1.00
- P51668 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D1 (P51668) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P51668
- Elsewhere: RCSB PDB 2C4P · PDBe 2C4P · UniProt P51668
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