Research workbench
The complex structure of PDZ domains in syntenin-1 with 4L peptide
Analyse The complex structure of PDZ domains in syntenin-1 with 4L peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A2P
- Type
- protein
- Length
- 680 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntenin-1; Syndecan-4
- UniProt
- Q9JI92, P34901
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Syntenin-1 | protein | 162 | 15% helix, 40% strand | Q9JI92 |
| E, F, G, H | Syndecan-4 | protein | 8 | 0% helix, 25% strand | P34901 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.68 | 0.82 | 58 | empty |
| 2 | 273 | 0.65 | 0.82 | 36 | empty |
| 3 | 67 | 0.33 | 0.75 | 12 | empty |
| 4 | 51 | 0.28 | 0.75 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1208 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1194 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 447 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 446 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 432 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5A2P · The complex structure of PDZ domains in syntenin-1 with 4L peptide · the same entry in another collection · chain H against H, TM-score 1.00
- Q9JI92 · AlphaFold monomer V2.0 prediction for syntenin-1 (Q9JI92) · a predicted model of the same protein · chain A against A, TM-score 0.91
- P34901 · AlphaFold monomer V2.0 prediction for syndecan-4 (P34901) · a predicted model of the same protein · chain E against A, TM-score 0.37
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 Q9JI92
- Every structure of UniProt P34901
- Elsewhere: RCSB PDB 5A2P · PDBe 5A2P · UniProt Q9JI92 · UniProt P34901
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