Research workbench
Crystal structure of the second bromodomain (BD2) of human TAF1 bound to dioxane
Analyse Crystal structure of the second bromodomain (BD2) of human TAF1 bound to dioxane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K42
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription initiation factor tfiid subunit 1
- EC
- 2.3.1.48, 2.7.11.1
- UniProt
- P21675
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcription initiation factor tfiid subunit 1 (EC 2.3.1.48, 2.7.11.1) | protein | 123 | 68% helix, 0% strand | P21675 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.51 | 0.82 | 20 | DIO, EDO |
| 2 | 116 | 0.48 | 0.79 | 19 | DIO, EDO |
| 3 | 69 | 0.43 | 0.81 | 17 | EDO |
| 4 | 56 | 0.29 | 0.74 | 12 | EDO |
Interfaces
1 interface between chains.
- A–B · 733 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 7K42 · Crystal structure of the second bromodomain (BD2) of human TAF1 bound to dioxane · the same entry in another collection · chain A against A, TM-score 1.00
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 P21675
- Elsewhere: RCSB PDB 7K42 · PDBe 7K42 · UniProt P21675
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