MolNFT v1 · #111856 · protein
Crystal structure of the syntenin PDZ1 and PDZ2 tandem in complex with the frizzled 7 C-terminal fragment and PIP2
4Z33 · Syntenin-1: “Crystal structure of the syntenin PDZ1 and PDZ2 tandem in complex with the frizzled 7 C-terminal fragment and…”. X-ray diffraction, 1 ligand (IP2), 3 pockets (best druggability 0.62). MolNFT v1 #111856 on GenesisL1: 3D…
- PDB
- 4Z33
- Type
- protein
- Length
- 341 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Syntenin-1; Lys-gly-glu-thr-ala-val
- UniProt
- O00560
- Ligands
- IP2
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Syntenin-1 | protein | 166 | 17% helix, 38% strand | O00560 |
| B | Syntenin-1 | protein | 165 | 19% helix, 38% strand | O00560 |
| C | Lys-gly-glu-thr-ala-val | protein | 6 | 0% helix, 33% strand | — |
| D | Lys-gly-glu-thr-ala-val | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- IP2 · D-myo-inositol-4,5-bisphosphate · ligand · chains A, C
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.62 | 0.83 | 31 | empty |
| 2 | 191 | 0.45 | 0.74 | 33 | empty |
| 3 | 65 | 0.32 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 495 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 345 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4Z33 · Crystal structure of the syntenin PDZ1 and PDZ2 tandem in complex with the Frizzled 7… · 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 4Z33 · PDBe 4Z33 · UniProt O00560
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