MolNFT v1 · #52119 · protein
Crystal structure of the human beta-2-syntrophin PDZ domain
2VRF: “Crystal structure of the human beta-2-syntrophin PDZ domain”. X-ray diffraction, 5 pockets (best druggability 0.57). MolNFT v1 #52119 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VRF
- Type
- protein
- Length
- 380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-syntrophin
- UniProt
- Q13425
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-2-syntrophin | protein | 95 | 18% helix, 41% strand | Q13425 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.57 | 0.79 | 39 | empty |
| 2 | 137 | 0.55 | 0.82 | 30 | empty |
| 3 | 138 | 0.52 | 0.81 | 36 | empty |
| 4 | 103 | 0.44 | 0.78 | 15 | empty |
| 5 | 57 | 0.34 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1199 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1178 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 424 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 Q13425
- Elsewhere: RCSB PDB 2VRF · PDBe 2VRF · UniProt Q13425
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