MolNFT v1 · #16880 · protein
Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.
1OBY · Syntenin 1: “Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.37). MolNFT v1 #16880 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1OBY
- Type
- protein
- Length
- 160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntenin 1; Syndecan-4
- UniProt
- O00560, P31431
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syntenin 1 | protein | 75 | 20% helix, 39% strand | O00560 |
| B | Syntenin 1 | protein | 74 | 20% helix, 39% strand | O00560 |
| P | Syndecan-4 | protein | 5 | 0% helix, 40% strand | P31431 |
| Q | Syndecan-4 | protein | 6 | 0% helix, 33% strand | P31431 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.37 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–Q · 446 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 440 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 241 Ų buried · 2 hydrogen bonds · protein-protein
- A–Q · 123 Ų buried · 0 hydrogen bonds · protein-protein
- B–P · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OBY · Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide. · the same entry in another collection · chain A against A, TM-score 1.00
- P31431 · AlphaFold monomer V2.0 prediction for syndecan-4 (P31431) · a predicted model of the same protein · chain P against A, TM-score 0.55
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
- Every structure of UniProt P31431
- Elsewhere: RCSB PDB 1OBY · PDBe 1OBY · UniProt O00560 · UniProt P31431
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