Research workbench
Crystal structure of tale homeobox domain transcription factor TGIF1 double alanine mutant bound to its consensus DNA
Analyse Crystal structure of tale homeobox domain transcription factor TGIF1 double… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FQQ
- Type
- protein + DNA
- Length
- 309 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox protein TGIF1; DNA (5'- D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3')
- UniProt
- Q15583
- Ligands
- CL
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein TGIF1 | protein | 60 | 72% helix, 0% strand | Q15583 |
| L, M, G, H | DNA (5'- D(P*AP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*T)-3') | dna | 16 | — | — |
| B, E | Homeobox protein TGIF1 | protein | 61 | 70% helix, 0% strand | Q15583 |
| D | Homeobox protein TGIF1 | protein | 63 | 68% helix, 0% strand | Q15583 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.58 | 0.78 | 21 | empty |
| 2 | 227 | 0.54 | 0.78 | 19 | empty |
| 3 | 61 | 0.31 | 0.76 | 15 | empty |
| 4 | 52 | 0.30 | 0.76 | 13 | empty |
Interfaces
11 interfaces between chains.
- G–H · 705 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- L–M · 696 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- G–E · 426 Ų buried · 12 hydrogen bonds · protein-nucleic
- G–D · 418 Ų buried · 5 hydrogen bonds · protein-nucleic
- H–E · 408 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6FQQ · Crystal structure of TALE homeobox domain transcription factor TGIF1 double alanine… · the same entry in another collection · chain E against E, TM-score 1.00
- Q15583 · AlphaFold monomer V2.0 prediction for homeobox protein TGIF1 (Q15583) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q15583
- Elsewhere: RCSB PDB 6FQQ · PDBe 6FQQ · UniProt Q15583
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