Research workbench
Crystal structure of human ubiquitin-conjugating enzyme UBCH5B
Analyse Crystal structure of human ubiquitin-conjugating enzyme UBCH5B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CLW
- Type
- protein
- Length
- 600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2
- EC
- 6.3.2.19
- UniProt
- P62837
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 150 | 37% helix, 17% strand | P62837 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.67 | 0.85 | 27 | empty |
| 2 | 186 | 0.50 | 0.77 | 21 | empty |
| 3 | 122 | 0.48 | 0.79 | 20 | empty |
| 4 | 187 | 0.45 | 0.74 | 33 | empty |
| 5 | 78 | 0.33 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 519 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 481 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 160 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 2CLW · Crystal structure of human ubiquitin-conjugating enzyme UbcH5B · 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 0.96
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 P62837
- Elsewhere: RCSB PDB 2CLW · PDBe 2CLW · UniProt P62837
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