Research workbench
TEAD4 (216-434);Y429F complexed with yap peptide (60-100) and myristoate (covalently bound) at 2.28A (P212121 crystal form); myristoylation was done by adding myr-CoA
Analyse TEAD4 (216-434);Y429F complexed with yap peptide (60-100) and myristoate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GEK
- Type
- protein
- Length
- 475 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional enhancer factor tef-3; Transcriptional coactivator YAP1
- UniProt
- Q15561, P46937
- Ligands
- MYR
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional enhancer factor tef-3 | protein | 202 | 17% helix, 54% strand | Q15561 |
| L | Transcriptional coactivator YAP1 | protein | 34 | 56% helix, 0% strand | P46937 |
| B | Transcriptional enhancer factor tef-3 | protein | 209 | 17% helix, 51% strand | Q15561 |
| M | Transcriptional coactivator YAP1 | protein | 30 | 37% helix, 0% strand | P46937 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.83 | 0.97 | 37 | MYR |
| 2 | 175 | 0.82 | 0.96 | 36 | MYR |
| 3 | 745 | 0.70 | 0.77 | 72 | empty |
| 4 | 112 | 0.41 | 0.76 | 19 | empty |
| 5 | 55 | 0.26 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–L · 1200 Ų buried · 11 hydrogen bonds · protein-protein
- B–M · 1157 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1008 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid (myristoylation).
Compared structures
- 6GEK · TEAD4 (216-434);Y429F complexed with yap peptide (60-100) and myristoate (covalently… · the same entry in another collection · chain M against M, TM-score 1.00
- Q15561 · AlphaFold monomer V2.0 prediction for transcriptional enhancer factor tef-3 (Q15561) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P46937 · AlphaFold monomer V2.0 prediction for transcriptional coactivator YAP1 (P46937) · a predicted model of the same protein · chain M against A, TM-score 0.46
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 Q15561
- Every structure of UniProt P46937
- Elsewhere: RCSB PDB 6GEK · PDBe 6GEK · UniProt Q15561 · UniProt P46937
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