Research workbench
Crystal structure of the human pcaf bromodomain in complex with compound 12
Analyse Crystal structure of the human pcaf bromodomain in complex with compound 12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J3O
- Type
- protein
- Length
- 211 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase KAT2B
- EC
- 2.3.1.48, 2.3.1.57
- UniProt
- Q92831
- Ligands
- B4L
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase KAT2B (EC 2.3.1.48, 2.3.1.57) | protein | 106 | 66% helix, 0% strand | Q92831 |
| B | Histone acetyltransferase KAT2B (EC 2.3.1.48, 2.3.1.57) | protein | 105 | 63% helix, 0% strand | Q92831 |
Ligands and binding sites
- B4L · 3-methyl-2-[[(3~{R})-1-methylpiperidin-3-yl]amino]-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.65 | 0.78 | 44 | empty |
| 2 | 108 | 0.57 | 0.85 | 21 | B4L |
| 3 | 107 | 0.53 | 0.82 | 19 | B4L |
| 4 | 55 | 0.34 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 788 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6J3O · Crystal structure of the human PCAF bromodomain in complex with compound 12 · 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 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 Q92831
- Elsewhere: RCSB PDB 6J3O · PDBe 6J3O · UniProt Q92831
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