MolNFT v1 · #25923 · protein
Crystal structure of the PDZ tandem of human syntenin in complex with tneyyv peptide
1W9O · Syntenin 1: “Crystal structure of the PDZ tandem of human syntenin in complex with tneyyv peptide”. X-ray diffraction, 1 ligand (BEZ), 4 pockets (best druggability 0.51). MolNFT v1 #25923 on GenesisL1: 3D structure, binding sites…
- PDB
- 1W9O
- Type
- protein
- Length
- 337 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntenin 1; Tneyyv peptide
- UniProt
- O00560
- Ligands
- BEZ
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syntenin 1 | protein | 164 | 16% helix, 39% strand | O00560 |
| B | Syntenin 1 | protein | 163 | 17% helix, 39% strand | O00560 |
| S, T | Tneyyv peptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.51 | 0.76 | 32 | empty |
| 2 | 86 | 0.41 | 0.77 | 16 | empty |
| 3 | 51 | 0.36 | 0.79 | 10 | empty |
| 4 | 50 | 0.29 | 0.76 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1105 Ų buried · 15 hydrogen bonds · protein-protein
- B–S · 488 Ų buried · 8 hydrogen bonds · protein-protein
- A–T · 461 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1W9O · Crystal structure of the PDZ tandem of human syntenin in complex with TNEYYV peptide · 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 1W9O · PDBe 1W9O · UniProt O00560
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