Research workbench
Crystal structure of the PDZ tandem of syntenin in complex with fragment C58
Analyse Crystal structure of the PDZ tandem of syntenin in complex with fragment C58 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R9H
- Type
- protein
- Length
- 651 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntenin-1
- UniProt
- O00560
- Ligands
- JVK, PO4
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Syntenin-1 | protein | 162 | 17% helix, 40% strand | O00560 |
| C | Syntenin-1 | protein | 164 | 17% helix, 39% strand | O00560 |
| D | Syntenin-1 | protein | 163 | 17% helix, 39% strand | O00560 |
Ligands and binding sites
- JVK · (2~{S})-2-[2-(4-chlorophenyl)sulfanylethanoylamino]-3-methyl-butanoic acid · ligand · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.63 | 0.81 | 39 | empty |
| 2 | 209 | 0.57 | 0.79 | 27 | empty |
| 3 | 225 | 0.54 | 0.77 | 31 | ACT |
| 4 | 102 | 0.39 | 0.76 | 21 | empty |
| 5 | 91 | 0.36 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1126 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1098 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 229 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6R9H · Crystal structure of the PDZ tandem of syntenin in complex with fragment C58 · the same entry in another collection · chain A against A, TM-score 1.00
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 6R9H · PDBe 6R9H · UniProt O00560
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.