Research workbench
Crystal structure of the complex of TRIM33 phd-bromo and H3(1-22) K9ME3K14ACK18AC histone peptide
Analyse Crystal structure of the complex of TRIM33 phd-bromo and H3(1-22)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U5O
- Type
- protein
- Length
- 1,675 residues
- Chains
- 16
- 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
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 189 | 41% helix, 3% strand | Q9UPN9 |
| B | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 189 | 44% helix, 3% strand | Q9UPN9 |
| C | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 195 | 38% helix, 3% strand | Q9UPN9 |
| D | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 187 | 42% helix, 3% strand | Q9UPN9 |
| E | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 188 | 41% helix, 3% strand | Q9UPN9 |
| G | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 187 | 41% helix, 3% strand | Q9UPN9 |
| H | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 191 | 41% helix, 3% strand | Q9UPN9 |
| I, J, K, L, M, N, O, P | Histone H3.1 | protein | 20 | 0% helix, 10% strand | P68431 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.76 | 0.84 | 51 | empty |
| 2 | 970 | 0.73 | 0.77 | 77 | empty |
| 3 | 524 | 0.71 | 0.80 | 59 | empty |
| 4 | 618 | 0.70 | 0.78 | 56 | empty |
| 5 | 564 | 0.69 | 0.78 | 47 | empty |
Interfaces
27 interfaces between chains.
- H–P · 1196 Ų buried · 22 hydrogen bonds · protein-protein
- D–L · 1194 Ų buried · 18 hydrogen bonds · protein-protein
- E–M · 1192 Ų buried · 22 hydrogen bonds · protein-protein
- C–K · 1178 Ų buried · 15 hydrogen bonds · protein-protein
- G–O · 1159 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (acetylation, methylation).
Compared structures
- 3U5O · Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone… · the same entry in another collection · chain P against P, 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 Q9UPN9
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 3U5O · PDBe 3U5O · UniProt Q9UPN9 · UniProt P68431
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