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Crystal structure of stilbene synthase from pinus sylvestris, complexed with methylmalonyl CoA
Analyse Crystal structure of stilbene synthase from pinus sylvestris, complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XET
- Type
- protein
- Length
- 1,540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropinosylvin synthase
- EC
- 2.3.1.-
- UniProt
- Q02323
- Ligands
- 3IO, MCA
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydropinosylvin synthase (EC 2.3.1.-) | protein | 387 | 42% helix, 24% strand | Q02323 |
| C | Dihydropinosylvin synthase (EC 2.3.1.-) | protein | 382 | 41% helix, 24% strand | Q02323 |
| D | Dihydropinosylvin synthase (EC 2.3.1.-) | protein | 384 | 42% helix, 24% strand | Q02323 |
Ligands and binding sites
- 3IO · 3-(1H-indol-3-yl)-2-oxopropanoic acid · ligand · 3 copies · chains A, B, C, D
- MCA · Methylmalonyl-coenzyme A · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.78 | 0.89 | 42 | 3IO |
| 2 | 300 | 0.78 | 0.89 | 44 | 3IO, MCA |
| 3 | 371 | 0.77 | 0.87 | 47 | 3IO |
| 4 | 922 | 0.76 | 0.79 | 99 | empty |
| 5 | 196 | 0.56 | 0.79 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3013 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 2973 Ų buried · 69 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 262 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1XET · Crystal structure of stilbene synthase from Pinus sylvestris, complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q02323 · AlphaFold monomer V2.0 prediction for pinosylvin synthase (Q02323) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q02323
- Elsewhere: RCSB PDB 1XET · PDBe 1XET · UniProt Q02323
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