Research workbench
The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of TRPV3
Analyse The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of TRPV3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QQN
- Type
- protein
- Length
- 838 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-1-SYNTROPHIN,ANNEXIN A2; Transient receptor potential cation channel subfamily V…
- UniProt
- Q9NSN8, P07355, Q8NET8
- Ligands
- CA
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-1-SYNTROPHIN,ANNEXIN A2 | protein | 413 | 58% helix, 10% strand | Q9NSN8, P07355 |
| C | Gamma-1-SYNTROPHIN,ANNEXIN A2 | protein | 414 | 60% helix, 9% strand | Q9NSN8, P07355 |
| B | Transient receptor potential cation channel subfamily V member 3 | protein | 5 | 0% helix, 60% strand | Q8NET8 |
| D | Transient receptor potential cation channel subfamily V member 3 | protein | 6 | 0% helix, 33% strand | Q8NET8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.76 | 0.78 | 98 | CA |
| 2 | 217 | 0.56 | 0.79 | 30 | empty |
| 3 | 110 | 0.49 | 0.81 | 23 | GOL |
| 4 | 270 | 0.48 | 0.73 | 32 | empty |
| 5 | 181 | 0.47 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 476 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 439 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7QQN · The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of TRPV3 · the same entry in another collection · chain A against A, TM-score 1.00
- P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain A against A, TM-score 0.78
- Q8NET8 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain B against A, TM-score 0.71
- Q9NSN8 · AlphaFold monomer V2.0 prediction for gamma-1-syntrophin (Q9NSN8) · a predicted model of the same protein · chain A against A, TM-score 0.29
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 Q9NSN8
- Every structure of UniProt P07355
- Every structure of UniProt Q8NET8
- Elsewhere: RCSB PDB 7QQN · PDBe 7QQN · UniProt Q9NSN8 · UniProt P07355 · UniProt Q8NET8
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