Research workbench
Crystal structure of human TBX5 in the DNA-bound and DNA- free form
Analyse Crystal structure of human TBX5 in the DNA-bound and DNA- free form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X6V
- Type
- protein + DNA
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-box transcription factor TBX5; 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3'…
- UniProt
- Q99593
- Ligands
- MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-box transcription factor TBX5 | protein | 177 | 20% helix, 39% strand | Q99593 |
| B | T-box transcription factor TBX5 | protein | 172 | 17% helix, 39% strand | Q99593 |
| C | 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3' | dna | 10 | — | — |
| D | 5'-D(*TP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP)-3' | dna | 11 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.74 | 0.79 | 69 | PE4 |
| 2 | 214 | 0.56 | 0.79 | 26 | empty |
| 3 | 134 | 0.46 | 0.77 | 23 | empty |
| 4 | 112 | 0.46 | 0.79 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 839 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 512 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 456 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- A–C · 408 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2X6V · Crystal structure of human TBX5 in the DNA-bound and DNA-free form · the same entry in another collection · chain A against A, TM-score 1.00
- Q99593 · AlphaFold monomer V2.0 prediction for T-box transcription factor TBX5 (Q99593) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q99593
- Elsewhere: RCSB PDB 2X6V · PDBe 2X6V · UniProt Q99593
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