Research workbench
Crystal structure of TRIM33 phd-bromodomain isoform B in complex with H3K10AC histone peptide.
Analyse Crystal structure of TRIM33 phd-bromodomain isoform B in complex with H3K10AC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZDD
- Type
- protein
- Length
- 186 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM33; Histone H3.X
- EC
- 6.3.2.-
- UniProt
- Q9UPN9, P0DPK5
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 176 | 39% helix, 4% strand | Q9UPN9 |
| D | Histone H3.X | protein | 10 | 0% helix, 40% strand | P0DPK5 |
Ligands and binding sites
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 | 69 | 0.46 | 0.82 | 16 | empty |
| 2 | 75 | 0.41 | 0.79 | 21 | EDO |
| 3 | 58 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–D · 570 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 7ZDD · Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K10ac 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 0.98
- P0DPK5 · AlphaFold monomer V2.0 prediction for histone H3.X (P0DPK5) · a predicted model of the same protein · chain D against A, TM-score 0.33
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 P0DPK5
- Elsewhere: RCSB PDB 7ZDD · PDBe 7ZDD · UniProt Q9UPN9 · UniProt P0DPK5
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