Research workbench
E3 ubiquitin-protein ligase RNF8 in complex with ubiquitin-conjugating enzyme E2 N and polyubiquitin-B
Analyse E3 ubiquitin-protein ligase RNF8 in complex with ubiquitin-conjugating enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WHV
- Type
- protein
- Length
- 1,349 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 N; E3 ubiquitin-protein ligase RNF8; Polyubiquitin-B
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P61088, O76064, P0CG47
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E, H, K | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 147 | 34% helix, 18% strand | P61088 |
| C | E3 ubiquitin-protein ligase RNF8 (EC 6.3.2.-) | protein | 136 | 63% helix, 10% strand | O76064 |
| D | E3 ubiquitin-protein ligase RNF8 (EC 6.3.2.-) | protein | 139 | 64% helix, 11% strand | O76064 |
| I, J | E3 ubiquitin-protein ligase RNF8 (EC 6.3.2.-) | protein | 101 | 50% helix, 14% strand | O76064 |
| A, F, G, L | Polyubiquitin-B | protein | 71 | 25% helix, 32% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains C, D, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.78 | 0.80 | 81 | empty |
| 2 | 898 | 0.77 | 0.80 | 83 | empty |
| 3 | 303 | 0.76 | 0.88 | 45 | empty |
| 4 | 502 | 0.74 | 0.82 | 50 | empty |
| 5 | 314 | 0.64 | 0.80 | 33 | empty |
Interfaces
22 interfaces between chains.
- C–D · 1236 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 968 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 462 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 447 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 394 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4WHV · E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and… · the same entry in another collection · chain L against L, TM-score 1.00
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 P61088
- Every structure of UniProt O76064
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 4WHV · PDBe 4WHV · UniProt P61088 · UniProt O76064 · UniProt P0CG47
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