Research workbench
E2~UBIQUITIN-hect
Analyse E2~UBIQUITIN-hect in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JW0
- Type
- protein
- Length
- 1,194 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; E3 ubiquitin-protein ligase NEDD4-like; Ubiquitin
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P62837, Q96PU5, P62988
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 146 | 36% helix, 18% strand | P62837 |
| C | E3 ubiquitin-protein ligase NEDD4-like (EC 6.3.2.-) | protein | 376 | 46% helix, 14% strand | Q96PU5 |
| D | E3 ubiquitin-protein ligase NEDD4-like (EC 6.3.2.-) | protein | 374 | 47% helix, 16% strand | Q96PU5 |
| X, Y | Ubiquitin | protein | 76 | 18% helix, 33% strand | P62988 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.77 | 0.80 | 91 | empty |
| 2 | 725 | 0.76 | 0.81 | 79 | empty |
| 3 | 607 | 0.67 | 0.76 | 65 | empty |
| 4 | 196 | 0.62 | 0.82 | 31 | empty |
| 5 | 52 | 0.61 | 0.93 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1382 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1335 Ų buried · 15 hydrogen bonds · protein-protein
- D–Y · 742 Ų buried · 9 hydrogen bonds · protein-protein
- C–X · 725 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 678 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3JW0 · E2~Ubiquitin-HECT · the same entry in another collection · chain Y against Y, 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 0.99
- Q96PU5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase NEDD4-like (Q96PU5) · a predicted model of the same protein · chain C against A, TM-score 0.67
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 Q96PU5
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 3JW0 · PDBe 3JW0 · UniProt P62837 · UniProt Q96PU5 · UniProt P62988
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