MolNFT v1 · #136195 · protein
Crystal structure of a UBCH5B~UB conjugate
5ULF · Ubiquitin-conjugating enzyme E2 D2: “Crystal structure of a UBCH5B~UB conjugate”. X-ray diffraction, 4 pockets (best druggability 0.61). MolNFT v1 #136195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ULF
- Type
- protein
- Length
- 454 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; Ubiquitin
- EC
- 2.3.2.23, 2.3.2.24
- UniProt
- P62837, P0CG47
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 151 | 37% helix, 19% strand | P62837 |
| B, D | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG47 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.61 | 0.75 | 50 | GOL |
| 2 | 168 | 0.53 | 0.79 | 25 | empty |
| 3 | 164 | 0.51 | 0.78 | 25 | empty |
| 4 | 53 | 0.26 | 0.73 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–C · 697 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 312 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 301 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 158 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
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 P62837
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5ULF · PDBe 5ULF · UniProt P62837 · UniProt P0CG47
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