Research workbench
Human TBX3, a transcription factor responsible for ulnar-mammary syndrome, bound to a palindromic DNA site
Analyse Human TBX3, a transcription factor responsible for ulnar-mammary syndrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H6F
- Type
- protein + DNA
- Length
- 418 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-box transcription factor TBX3; 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*…
- UniProt
- O15119
- Ligands
- MG
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-box transcription factor TBX3 | protein | 184 | 21% helix, 36% strand | O15119 |
| B | T-box transcription factor TBX3 | protein | 186 | 20% helix, 36% strand | O15119 |
| C, D | 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3' | dna | 24 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.63 | 0.75 | 53 | empty |
| 2 | 295 | 0.58 | 0.78 | 30 | empty |
| 3 | 247 | 0.55 | 0.77 | 31 | empty |
| 4 | 118 | 0.51 | 0.81 | 19 | empty |
| 5 | 62 | 0.31 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 970 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- A–D · 514 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 507 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 491 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 434 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1H6F · Human TBX3, a transcription factor responsible for ulnar-mammary syndrome, bound to a… · the same entry in another collection · chain A against A, TM-score 1.00
- O15119 · AlphaFold monomer V2.0 prediction for T-box transcription factor TBX3 (O15119) · a predicted model of the same protein · chain B 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 O15119
- Elsewhere: RCSB PDB 1H6F · PDBe 1H6F · UniProt O15119
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.