MolNFT v1 · #51548 · protein
Structure of strictosidine synthase in complex with inhibitor
2VAQ: “Structure of strictosidine synthase in complex with inhibitor”. X-ray diffraction, 1 ligand (VAW), 7 pockets (best druggability 0.72). MolNFT v1 #51548 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VAQ
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Strictosidine synthase
- EC
- 4.3.3.2
- UniProt
- P68175
- Ligands
- VAW
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strictosidine synthase (EC 4.3.3.2) | protein | 305 | 7% helix, 48% strand | P68175 |
Ligands and binding sites
- VAW · (2S,3R,4S)-methyl 4-(2-(2-(1H-indol-3-yl)ethylamino)ethyl)-2-((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.72 | 0.85 | 33 | VAW |
| 2 | 248 | 0.69 | 0.85 | 28 | VAW |
| 3 | 182 | 0.58 | 0.82 | 25 | empty |
| 4 | 193 | 0.57 | 0.80 | 25 | empty |
| 5 | 158 | 0.47 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 794 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 P68175
- Elsewhere: RCSB PDB 2VAQ · PDBe 2VAQ · UniProt P68175
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