Research workbench
The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of pten
Analyse The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of pten in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PC7
- Type
- protein
- Length
- 816 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-1-SYNTROPHIN,ANNEXIN A2; Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and…
- EC
- 3.1.3.16, 3.1.3.48, 3.1.3.67
- UniProt
- Q9NSN8, P07355, P60484
- Ligands
- CA
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-1-SYNTROPHIN,ANNEXIN A2 | protein | 398 | 62% helix, 8% strand | Q9NSN8, P07355 |
| B | Gamma-1-SYNTROPHIN,ANNEXIN A2 | protein | 404 | 62% helix, 9% strand | Q9NSN8, P07355 |
| E | Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase pten (EC 3.1.3.16, 3.1.3.48, 3.1.3.67) | protein | 10 | 0% helix, 30% strand | P60484 |
| F | Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase pten (EC 3.1.3.16, 3.1.3.48, 3.1.3.67) | protein | 4 | 0% helix, 50% strand | P60484 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.65 | 0.77 | 48 | GOL |
| 2 | 89 | 0.57 | 0.86 | 20 | empty |
| 3 | 78 | 0.52 | 0.85 | 21 | GOL |
| 4 | 126 | 0.51 | 0.81 | 33 | GOL |
| 5 | 106 | 0.51 | 0.82 | 25 | GOL |
Interfaces
3 interfaces between chains.
- A–E · 619 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 440 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 431 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 7PC7 · The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of PTEN · the same entry in another collection · chain A against A, TM-score 1.00
- P60484 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3,4,5-trisphosphate… · a predicted model of the same protein · chain F against A, TM-score 0.95
- P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain B against A, TM-score 0.81
- Q9NSN8 · AlphaFold monomer V2.0 prediction for gamma-1-syntrophin (Q9NSN8) · a predicted model of the same protein · chain A against A, TM-score 0.27
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 P60484
- Elsewhere: RCSB PDB 7PC7 · PDBe 7PC7 · UniProt Q9NSN8 · UniProt P07355 · UniProt P60484
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