Research workbench
The PDZ domain of SNTG1 complexed with the phosphomimetic mutant PDZ- binding motif of RSK1
Analyse The PDZ domain of SNTG1 complexed with the phosphomimetic mutant PDZ- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PC8
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-1-SYNTROPHIN,ANNEXIN A2; Ribosomal protein S6 kinase alpha-1
- EC
- 2.7.11.1
- UniProt
- Q9NSN8, P07355, Q15418
- Ligands
- CA
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-1-SYNTROPHIN,ANNEXIN A2 | protein | 413 | 59% helix, 10% strand | Q9NSN8, P07355 |
| B | Gamma-1-SYNTROPHIN,ANNEXIN A2 | protein | 409 | 60% helix, 9% strand | Q9NSN8, P07355 |
| C | Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) | protein | 8 | 0% helix, 38% strand | Q15418 |
| D | Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) | protein | 6 | 0% helix, 50% strand | Q15418 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.68 | 0.77 | 85 | GOL |
| 2 | 209 | 0.52 | 0.77 | 31 | GOL |
| 3 | 203 | 0.51 | 0.77 | 27 | empty |
| 4 | 166 | 0.50 | 0.78 | 35 | GOL |
| 5 | 112 | 0.46 | 0.79 | 26 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 655 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 605 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 506 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7PC8 · The PDZ domain of SNTG1 complexed with the phosphomimetic mutant PDZ-binding motif of RSK1 · 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 B against A, TM-score 0.79
- Q15418 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-1 (Q15418) · a predicted model of the same protein · chain D against A, TM-score 0.73
- Q9NSN8 · AlphaFold monomer V2.0 prediction for gamma-1-syntrophin (Q9NSN8) · a predicted model of the same protein · chain B against A, TM-score 0.26
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 Q15418
- Elsewhere: RCSB PDB 7PC8 · PDBe 7PC8 · UniProt Q9NSN8 · UniProt P07355 · UniProt Q15418
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