MolNFT v1 · #51489 · protein
Structure of strictosidine synthase in complex with strictosidine
2V91: “Structure of strictosidine synthase in complex with strictosidine”. X-ray diffraction, 1 ligand (S55), 7 pockets (best druggability 0.69). MolNFT v1 #51489 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2V91
- Type
- protein
- Length
- 604 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
- S55
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Strictosidine synthase (EC 4.3.3.2) | protein | 302 | 9% helix, 48% strand | P68175 |
Ligands and binding sites
- S55 · Methyl (2S,3R,4S)-3-ethyl-2-(beta-D-glucopyranosyloxy)-4-[(1S)-2,3,4,9-tetrahydro-1H-beta-carbolin-1-ylmethyl]-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 | 263 | 0.69 | 0.84 | 33 | S55 |
| 2 | 235 | 0.66 | 0.83 | 28 | S55 |
| 3 | 189 | 0.57 | 0.80 | 22 | empty |
| 4 | 194 | 0.56 | 0.80 | 23 | empty |
| 5 | 164 | 0.47 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 630 Ų buried · 9 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 2V91 · PDBe 2V91 · UniProt P68175
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