Research workbench
Crystal structure of the PDZ tandem of human syntenin in complex with tneyyv peptide
Analyse Crystal structure of the PDZ tandem of human syntenin in complex with tneyyv… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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