MolNFT v1 · #141298 · protein
VGLL1-TEAD4 core complex
5Z2Q · Transcription cofactor vestigial-like protein 1: “VGLL1-TEAD4 core complex”. X-ray diffraction, 1 ligand (PO4), 11 pockets (best druggability 0.83). MolNFT v1 #141298 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Z2Q
- Type
- protein
- Length
- 505 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription cofactor vestigial-like protein 1; Transcriptional enhancer factor tef-3
- UniProt
- Q99NC0, Q62296
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Transcription cofactor vestigial-like protein 1 | protein | 35 | 37% helix, 29% strand | Q99NC0 |
| D | Transcription cofactor vestigial-like protein 1 | protein | 36 | 36% helix, 28% strand | Q99NC0 |
| A | Transcriptional enhancer factor tef-3 | protein | 219 | 17% helix, 47% strand | Q62296 |
| B | Transcriptional enhancer factor tef-3 | protein | 215 | 19% helix, 47% strand | Q62296 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.83 | 0.97 | 36 | empty |
| 2 | 161 | 0.83 | 0.97 | 28 | empty |
| 3 | 245 | 0.61 | 0.81 | 40 | empty |
| 4 | 56 | 0.46 | 0.84 | 17 | empty |
| 5 | 133 | 0.40 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- D–A · 1094 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 1076 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 846 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5Z2Q · Vgll1-TEAD4 core complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q62296 · AlphaFold monomer V2.0 prediction for transcriptional enhancer factor tef-3 (Q62296) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q99NC0 · AlphaFold monomer V2.0 prediction for transcription cofactor vestigial-like protein 1… · a predicted model of the same protein · chain D against A, TM-score 0.89
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 Q99NC0
- Every structure of UniProt Q62296
- Elsewhere: RCSB PDB 5Z2Q · PDBe 5Z2Q · UniProt Q99NC0 · UniProt Q62296
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