Research workbench
Crystal structure of human pcaf bromodomain in complex with fragment ZB1916 (fragment 10)
Analyse Crystal structure of human pcaf bromodomain in complex with fragment ZB1916… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FE6
- Type
- protein
- Length
- 219 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase KAT2B
- EC
- 2.3.1.48
- UniProt
- Q92831
- Ligands
- 5WZ
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 109 | 65% helix, 0% strand | Q92831 |
| B | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 110 | 67% helix, 0% strand | Q92831 |
Ligands and binding sites
- 5WZ · (4-azanylpiperidin-1-yl)-cyclopropyl-methanone · ligand · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.68 | 0.79 | 37 | EDO |
| 2 | 135 | 0.53 | 0.81 | 22 | DMS |
| 3 | 116 | 0.53 | 0.82 | 19 | EDO, 5WZ |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5FE6 · Crystal structure of human PCAF bromodomain in complex with fragment ZB1916 (fragment 10) · the same entry in another collection · chain A against A, TM-score 1.00
- Q92831 · AlphaFold monomer V2.0 prediction for histone acetyltransferase KAT2B (Q92831) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q92831
- Elsewhere: RCSB PDB 5FE6 · PDBe 5FE6 · UniProt Q92831
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