MolNFT v1 · #119609 · protein
The complex structure of syntenin-1 PDZ domain with C-terminal extension
5G1D: “The complex structure of syntenin-1 PDZ domain with C-terminal extension”. X-ray diffraction, 3 pockets (best druggability 0.54). MolNFT v1 #119609 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5G1D
- Type
- protein
- Length
- 351 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntenin-1; Syndecan-4
- UniProt
- Q9JI92
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syntenin-1 | protein | 168 | 20% helix, 38% strand | Q9JI92 |
| B | Syntenin-1 | protein | 167 | 20% helix, 37% strand | Q9JI92 |
| C, D | Syndecan-4 | protein | 8 | 0% helix, 25% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.54 | 0.82 | 22 | empty |
| 2 | 94 | 0.45 | 0.80 | 21 | empty |
| 3 | 65 | 0.34 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1136 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 401 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 396 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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
- Elsewhere: RCSB PDB 5G1D · PDBe 5G1D · UniProt Q9JI92
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