Research workbench
Crystal structure of TRIM24 phd-bromodomain complexed with 1-methyl-5- (2-methyl-1 3-thiazol-4-yl)-2 3-dihydro-1H-indol-2-one (1)
Analyse Crystal structure of TRIM24 phd-bromodomain complexed with 1-methyl-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YAB
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription intermediary factor 1-alpha
- EC
- 6.3.2.-
- UniProt
- O15164
- Ligands
- 4CN, ZN, SO4
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription intermediary factor 1-alpha (EC 6.3.2.-) | protein | 178 | 42% helix, 2% strand | O15164 |
| B | Transcription intermediary factor 1-alpha (EC 6.3.2.-) | protein | 174 | 42% helix, 2% strand | O15164 |
Ligands and binding sites
- 4CN · 1-methyl-5-(2-methyl-1,3-thiazol-4-yl)-1,3-dihydro-2H-indol-2-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.44 | 0.83 | 15 | 4CN |
| 2 | 111 | 0.42 | 0.77 | 20 | empty |
| 3 | 60 | 0.39 | 0.80 | 16 | 4CN |
| 4 | 54 | 0.24 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 128 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4YAB · Crystal structure of TRIM24 PHD-bromodomain complexed with 1-methyl-5-(2-methyl-1… · the same entry in another collection · chain A against A, TM-score 1.00
- O15164 · AlphaFold monomer V2.0 prediction for transcription intermediary factor 1-alpha (O15164) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O15164
- Elsewhere: RCSB PDB 4YAB · PDBe 4YAB · UniProt O15164
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