Research workbench
The PDZ domain of SNTG2 complexed with the phosphorylated PDZ-binding motif of RSK1
Analyse The PDZ domain of SNTG2 complexed with the phosphorylated PDZ-binding motif of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QQL
- Type
- protein
- Length
- 1,204 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-2-SYNTROPHIN,ANNEXIN A2; Ribosomal protein S6 kinase alpha-1
- EC
- 2.7.11.1
- UniProt
- Q9NY99, P07355, Q15418
- Ligands
- CA
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Gamma-2-SYNTROPHIN,ANNEXIN A2 | protein | 396 | 63% helix, 9% strand | Q9NY99, P07355 |
| F, D, E | Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) | protein | 5 | 0% helix, 60% strand | Q15418 |
| A | Gamma-2-SYNTROPHIN,ANNEXIN A2 | protein | 398 | 61% helix, 8% strand | Q9NY99, P07355 |
| B | Gamma-2-SYNTROPHIN,ANNEXIN A2 | protein | 395 | 62% helix, 10% strand | Q9NY99, P07355 |
Ligands and binding sites
- CA · Calcium ion · metal · 14 copies · chains C, A, B
- GOL · Glycerol · additive · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.80 | 0.82 | 82 | empty |
| 2 | 980 | 0.74 | 0.77 | 82 | empty |
| 3 | 241 | 0.62 | 0.81 | 24 | empty |
| 4 | 385 | 0.61 | 0.77 | 45 | empty |
| 5 | 321 | 0.57 | 0.76 | 34 | empty |
Interfaces
7 interfaces between chains.
- C–A · 553 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 543 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 434 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 417 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 405 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 7QQL · The PDZ domain of SNTG2 complexed with the phosphorylated PDZ-binding motif of RSK1 · the same entry in another collection · chain C against C, TM-score 1.00
- Q15418 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-1 (Q15418) · a predicted model of the same protein · chain F against A, TM-score 0.80
- 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
- Q9NY99 · AlphaFold monomer V2.0 prediction for gamma-2-syntrophin (Q9NY99) · a predicted model of the same protein · chain C against A, TM-score 0.28
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 Q9NY99
- Every structure of UniProt P07355
- Every structure of UniProt Q15418
- Elsewhere: RCSB PDB 7QQL · PDBe 7QQL · UniProt Q9NY99 · UniProt P07355 · UniProt Q15418
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