MolNFT v1 · #162447 · protein
Crystal structure of the PDZ tandem of syntenin in complex with fragment C58
6R9H · Syntenin-1: “Crystal structure of the PDZ tandem of syntenin in complex with fragment C58”. X-ray diffraction, 2 ligands (JVK, PO4), 10 pockets (best druggability 0.63). MolNFT v1 #162447 on GenesisL1: 3D structure, binding sites…
- 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
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