MolNFT v1 · #161084 · protein
TEAD4(216-434) complexed with optimized peptide 9 and myristoate (covalently bound) at 2.01A resolution: structure-based design of potent linear peptide inhibitors of the yap-tead protein-protein interaction derived from the yap omega-loop sequence
6Q36 · Transcriptional enhancer factor tef-3: “TEAD4(216-434) complexed with optimized peptide 9 and myristoate (covalently bound) at 2.01A resolution…”. X-ray diffraction, 5 ligands (ACE, 2JH, MYR), 7 pockets (best druggability 0.83).…
- PDB
- 6Q36
- Type
- protein
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional enhancer factor tef-3; ACE-pro-6CW-arg-leu-arg-lys-2JH-hyp-asp-ser-phe-aln…
- UniProt
- Q15561
- Ligands
- ACE, 2JH, MYR, PO4, NH2
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional enhancer factor tef-3 | protein | 215 | 18% helix, 50% strand | Q15561 |
| B | Transcriptional enhancer factor tef-3 | protein | 214 | 16% helix, 51% strand | Q15561 |
| C, D | ACE-pro-6CW-arg-leu-arg-lys-2JH-hyp-asp-ser-phe-aln-lys- glu-pro-NH2 | protein | 14 | 50% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, D
- 2JH · 3-cyclobutyl-L-alanine · ligand · 2 copies · chains A, C, B, D
- MYR · Myristic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.83 | 0.94 | 37 | MYR |
| 2 | 223 | 0.83 | 0.95 | 38 | MYR |
| 3 | 719 | 0.71 | 0.78 | 76 | PO4 |
| 4 | 212 | 0.51 | 0.76 | 29 | PO4 |
| 5 | 53 | 0.37 | 0.79 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1053 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 800 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 779 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 modified, 2 lipid (covalent ligand, nonstandard, myristoylation, hydroxylation).
Compared structures
- 6Q36 · TEAD4(216-434) complexed with optimized peptide 9 and myristoate (covalently bound) at… · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.97
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
- Elsewhere: RCSB PDB 6Q36 · PDBe 6Q36 · UniProt Q15561
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