MolNFT v1 · #66869 · protein
Crystal structure of the bromodomain of human EP300
3I3J · Histone acetyltransferase P300: “Crystal structure of the bromodomain of human EP300”. X-ray diffraction, 2 ligands (CL, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #66869 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3I3J
- Type
- protein
- Length
- 1,362 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase P300
- EC
- 2.3.1.48
- UniProt
- Q09472
- Ligands
- CL, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, K | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 114 | 68% helix, 0% strand | Q09472 |
| B | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 114 | 68% helix, 0% strand | Q09472 |
| D, G, H, J, L | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 113 | 68% helix, 0% strand | Q09472 |
| E, I | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 115 | 68% helix, 0% strand | Q09472 |
| F | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 111 | 68% helix, 0% strand | Q09472 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, E, G
- SO4 · Sulfate ion · ion · 2 copies · chains E, L
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.80 | 0.84 | 75 | empty |
| 2 | 811 | 0.80 | 0.83 | 95 | empty |
| 3 | 480 | 0.77 | 0.84 | 54 | empty |
| 4 | 236 | 0.67 | 0.84 | 33 | empty |
| 5 | 163 | 0.66 | 0.86 | 26 | empty |
Interfaces
25 interfaces between chains.
- A–C · 962 Ų buried · 9 hydrogen bonds · protein-protein
- I–K · 938 Ų buried · 7 hydrogen bonds · protein-protein
- E–G · 884 Ų buried · 8 hydrogen bonds · protein-protein
- D–J · 875 Ų buried · 7 hydrogen bonds · protein-protein
- F–H · 830 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3I3J · Crystal Structure of the Bromodomain of Human EP300 · the same entry in another collection · chain L against L, 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 Q09472
- Elsewhere: RCSB PDB 3I3J · PDBe 3I3J · UniProt Q09472
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