Research workbench
Structure of the hoip-RBR/UBCH5B~UBIQUITIN transfer complex
Analyse Structure of the hoip-RBR/UBCH5B~UBIQUITIN transfer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EDV
- Type
- protein
- Length
- 1,363 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31; Ubiquitin-conjugating enzyme E2 D2; Polyubiquitin-B
- EC
- 6.3.2.-, 2.3.2.23, 2.3.2.24
- UniProt
- Q96EP0, P62837, P0CG47
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 286 | 34% helix, 15% strand | Q96EP0 |
| B | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 333 | 35% helix, 14% strand | Q96EP0 |
| C | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 145 | 37% helix, 19% strand | P62837 |
| D | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 148 | 38% helix, 18% strand | P62837 |
| E, F, G, H | Polyubiquitin-B | protein | 76 | 24% helix, 37% strand | P0CG47 |
| I | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 147 | 37% helix, 18% strand | P62837 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.85 | 0.88 | 85 | empty |
| 2 | 736 | 0.85 | 0.88 | 69 | empty |
| 3 | 264 | 0.73 | 0.87 | 41 | empty |
| 4 | 251 | 0.72 | 0.87 | 39 | empty |
| 5 | 568 | 0.70 | 0.79 | 53 | empty |
Interfaces
15 interfaces between chains.
- A–E · 1473 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1370 Ų buried · 18 hydrogen bonds · protein-protein
- A–G · 1069 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 1054 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 989 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 isopeptide (isopeptide).
Compared structures
- 5EDV · Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex · the same entry in another collection · chain I against I, 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 C against A, TM-score 0.99
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 Q96EP0
- Every structure of UniProt P62837
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5EDV · PDBe 5EDV · UniProt Q96EP0 · UniProt P62837 · UniProt P0CG47
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