MolNFT v1 · #80726 · protein
Crystal structure of the complex of TRIM33 phd-bromo and H3(1-20) K9ME3K14AC histone peptide
3U5N · E3 ubiquitin-protein ligase TRIM33: “Crystal structure of the complex of TRIM33 phd-bromo and H3(1-20) K9ME3K14AC histone peptide”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.74). MolNFT v1 #80726 on GenesisL1…
- PDB
- 3U5N
- Type
- protein
- Length
- 401 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM33; Histone H3.1
- EC
- 6.3.2.-
- UniProt
- Q9UPN9, P68431
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 185 | 41% helix, 4% strand | Q9UPN9 |
| C | Histone H3.1 | protein | 10 | 0% helix, 50% strand | P68431 |
| B | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 186 | 41% helix, 4% strand | Q9UPN9 |
| D | Histone H3.1 | protein | 20 | 15% helix, 20% strand | P68431 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.74 | 0.77 | 93 | empty |
| 2 | 119 | 0.52 | 0.81 | 21 | empty |
| 3 | 129 | 0.48 | 0.79 | 22 | empty |
| 4 | 74 | 0.33 | 0.75 | 17 | empty |
| 5 | 65 | 0.28 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–D · 740 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 661 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 257 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 212 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (methylation, acetylation).
Compared structures
- 3U5N · Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone… · the same entry in another collection · chain C against C, 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 B against A, TM-score 0.98
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 P68431
- Elsewhere: RCSB PDB 3U5N · PDBe 3U5N · UniProt Q9UPN9 · UniProt P68431
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