Research workbench
Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A LYS15 in complex with RNF169 (653-708)
Analyse Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A LYS15 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VEY
- Type
- protein
- Length
- 321 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H2B type 1-J,HISTONE H2A type 1-B/E; Polyubiquitin-B; E3 ubiquitin-protein ligase…
- EC
- 2.3.2.27
- UniProt
- P06899, P04908, P0CG47, Q8NCN4
- Pockets
- 2 · best druggability 0.51
Structure
solution nmr · 3 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H2B type 1-J,HISTONE H2A type 1-B/E | protein | 186 | 69% helix, 4% strand | P06899, P04908 |
| B | Polyubiquitin-B | protein | 76 | 25% helix, 34% strand | P0CG47 |
| C | E3 ubiquitin-protein ligase RNF169 (EC 2.3.2.27) | protein | 59 | 51% helix, 0% strand | Q8NCN4 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.51 | 0.77 | 19 | empty |
| 2 | 179 | 0.42 | 0.73 | 33 | empty |
Interfaces
3 interfaces between chains.
- B–C · 629 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 217 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5VEY · Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NCN4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF169 (Q8NCN4) · a predicted model of the same protein · chain C against A, TM-score 0.55
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 P06899
- Every structure of UniProt P04908
- Every structure of UniProt P0CG47
- Every structure of UniProt Q8NCN4
- Elsewhere: RCSB PDB 5VEY · PDBe 5VEY · UniProt P06899 · UniProt P04908 · UniProt P0CG47 · UniProt Q8NCN4
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