Research workbench
SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z1454310449
Analyse SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FSV
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Homo sapiens
- Molecule
- Syntenin-1
- UniProt
- O00560
- Ligands
- UQS, DGL, GLY, ALA, SO4
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.25 · 2 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Syntenin-1 | protein | 191 | 23% helix, 34% strand | O00560 |
| B, C | Syntenin-1 | protein | 193 | 21% helix, 34% strand | O00560 |
Ligands and binding sites
- UQS · N-[(2-fluorophenyl)methyl]-1H-pyrazol-4-amine · ligand · 4 copies · chains A, B, C, D
- DGL · D-glutamic acid · ligand · 2 copies · chains B, D
- GLY · Glycine · ligand · 2 copies · chains C, D
- ALA · Alanine · ligand · chains D
- SO4 · Sulfate ion · ion · chains D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.74 | 0.90 | 39 | EDO |
| 2 | 108 | 0.51 | 0.82 | 19 | EDO |
| 3 | 58 | 0.48 | 0.85 | 14 | empty |
| 4 | 164 | 0.47 | 0.76 | 20 | empty |
| 5 | 91 | 0.45 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1291 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 738 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 115 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- O00560 · AlphaFold monomer V2.0 prediction for syntenin-1 (O00560) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O00560
- Elsewhere: RCSB PDB 7FSV · PDBe 7FSV · UniProt O00560
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