MolNFT v1 · #80728 · protein
Crystal structure of the complex of TRIM33 phd-bromo and H3(1-28) K9ME3K14ACK18ACK23AC histone peptide
3U5P · E3 ubiquitin-protein ligase TRIM33: “Crystal structure of the complex of TRIM33 phd-bromo and H3(1-28) K9ME3K14ACK18ACK23AC histone peptide”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.72). MolNFT v1 #80728 on…
- PDB
- 3U5P
- Type
- protein
- Length
- 1,641 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 0.72
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 188 | 41% helix, 4% strand | Q9UPN9 |
| I, L, O | Histone H3.1 | protein | 18 | 0% helix, 17% strand | P68431 |
| J, K, N, P | Histone H3.1 | protein | 16 | 0% helix, 25% strand | P68431 |
| M | Histone H3.1 | protein | 19 | 0% helix, 21% 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.72 | 0.76 | 110 | empty |
| 2 | 791 | 0.69 | 0.76 | 65 | empty |
| 3 | 800 | 0.69 | 0.76 | 58 | empty |
| 4 | 845 | 0.69 | 0.75 | 65 | empty |
| 5 | 354 | 0.58 | 0.76 | 34 | empty |
Interfaces
27 interfaces between chains.
- H–P · 1147 Ų buried · 21 hydrogen bonds · protein-protein
- C–K · 1126 Ų buried · 19 hydrogen bonds · protein-protein
- E–M · 1123 Ų buried · 17 hydrogen bonds · protein-protein
- G–O · 1119 Ų buried · 22 hydrogen bonds · protein-protein
- A–I · 1118 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (acetylation, methylation).
Compared structures
- 3U5P · Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac… · 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 3U5P · PDBe 3U5P · UniProt Q9UPN9 · UniProt P68431
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