Research workbench
Crystal structure of TRIM33 phd-bromodomain isoform B in complex with H3K9AC histone peptide
Analyse Crystal structure of TRIM33 phd-bromodomain isoform B in complex with H3K9AC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MR8
- Type
- protein
- Length
- 195 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM33; Histone H3
- EC
- 6.3.2.-
- UniProt
- Q9UPN9, Q5TEC6
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 186 | 39% helix, 3% strand | Q9UPN9 |
| C | Histone H3 | protein | 9 | 0% helix, 44% strand | Q5TEC6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.48 | 0.77 | 22 | empty |
| 2 | 65 | 0.47 | 0.83 | 17 | empty |
| 3 | 69 | 0.43 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 618 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 5MR8 · Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K9ac histone… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UPN9 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM33 (Q9UPN9) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q5TEC6 · AlphaFold monomer V2.0 prediction for histone HIST2H3PS2 (Q5TEC6) · a predicted model of the same protein · chain C against A, TM-score 0.30
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 Q9UPN9
- Every structure of UniProt Q5TEC6
- Elsewhere: RCSB PDB 5MR8 · PDBe 5MR8 · UniProt Q9UPN9 · UniProt Q5TEC6
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