MolNFT v1 · #120401 · protein + DNA
Crystal structure of transcription factor TEAD4 in complex with M-cat DNA
5GZB · Transcriptional enhancer factor tef-3: “Crystal structure of transcription factor TEAD4 in complex with M-cat DNA”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.39). MolNFT v1 #120401 on GenesisL1: 3D structure…
- PDB
- 5GZB
- Type
- protein + DNA
- Length
- 117 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional enhancer factor tef-3; DNA (5'-D(*TP*TP*GP*CP*AP*TP*TP*CP*CP*TP*CP*TP*C)-3…
- UniProt
- Q15561
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional enhancer factor tef-3 | protein | 91 | 66% helix, 4% strand | Q15561 |
| B | DNA (5'-D(*TP*TP*GP*CP*AP*TP*TP*CP*CP*TP*CP*TP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*TP*GP*CP*AP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.39 | 0.80 | 11 | empty |
| 2 | 57 | 0.34 | 0.78 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 586 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 577 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–C · 545 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 5GZB · Crystal Structure of Transcription Factor TEAD4 in Complex with M-CAT DNA · 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 A against A, TM-score 0.80
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 5GZB · PDBe 5GZB · UniProt Q15561
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