MolNFT v1 · #110911 · protein
Crystal structure of TRIM24 phd-bromodomain complexed with N-(1,3- dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl)-4-methoxybenzene- 1-sulfonamide (5B)
4YAT · Transcription intermediary factor 1-alpha: “Crystal structure of TRIM24 phd-bromodomain complexed with N-(1,3…”. X-ray diffraction, 2 ligands (4A8, ZN), 5 pockets (best druggability 0.55). MolNFT v1 #110911 on GenesisL1: 3D…
- PDB
- 4YAT
- Type
- protein
- Length
- 345 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
- 4A8, ZN
- Pockets
- 5 · best druggability 0.55
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 | 173 | 42% helix, 2% strand | O15164 |
| B | Transcription intermediary factor 1-alpha (EC 6.3.2.-) | protein | 172 | 42% helix, 2% strand | O15164 |
Ligands and binding sites
- 4A8 · N-(1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)-4-methoxybenzenesulfonamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.55 | 0.76 | 23 | empty |
| 2 | 152 | 0.44 | 0.76 | 22 | empty |
| 3 | 55 | 0.41 | 0.81 | 15 | 4A8 |
| 4 | 50 | 0.40 | 0.81 | 14 | 4A8 |
| 5 | 67 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 683 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4YAT · Crystal structure of TRIM24 PHD-bromodomain complexed with… · 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 0.98
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 O15164
- Elsewhere: RCSB PDB 4YAT · PDBe 4YAT · UniProt O15164
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