Research workbench
Complex structure of TRIM24 phd-bromodomain and inhibitor 2
Analyse Complex structure of TRIM24 phd-bromodomain and inhibitor 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H1U
- Type
- protein
- Length
- 701 residues
- Chains
- 4
- 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
- 6KT, ZN
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transcription intermediary factor 1-alpha (EC 6.3.2.-) | protein | 174 | 43% helix, 2% strand | O15164 |
| A | Transcription intermediary factor 1-alpha (EC 6.3.2.-) | protein | 174 | 43% helix, 2% strand | O15164 |
| C | Transcription intermediary factor 1-alpha (EC 6.3.2.-) | protein | 177 | 43% helix, 2% strand | O15164 |
| D | Transcription intermediary factor 1-alpha (EC 6.3.2.-) | protein | 176 | 43% helix, 2% strand | O15164 |
Ligands and binding sites
- 6KT · 2-amino-1,3-benzothiazole-6-carboxamide · ligand · 4 copies · chains B, A, C, D
- ZN · Zinc ion · metal · 8 copies · chains B, A, C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.59 | 0.75 | 50 | 6KT |
| 2 | 269 | 0.52 | 0.75 | 35 | empty |
| 3 | 225 | 0.51 | 0.76 | 24 | empty |
| 4 | 62 | 0.46 | 0.83 | 19 | 6KT |
| 5 | 127 | 0.43 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–A · 648 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 117 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5H1U · Complex structure of TRIM24 PHD-bromodomain and inhibitor 2 · the same entry in another collection · chain D against D, 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 5H1U · PDBe 5H1U · UniProt O15164
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