MolNFT v1 · #79118 · protein
Crystal structure of tomato methylketone synthase I complexed with 2- tridecanone
3STW · Methylketone synthase 1: “Crystal structure of tomato methylketone synthase I complexed with 2- tridecanone”. X-ray diffraction, 1 ligand (2TD), 4 pockets (best druggability 0.77). MolNFT v1 #79118 on GenesisL1: 3D structure…
- PDB
- 3STW
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylketone synthase 1
- UniProt
- E0YCS2
- Ligands
- 2TD
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylketone synthase 1 | protein | 258 | 43% helix, 17% strand | E0YCS2 |
| B | Methylketone synthase 1 | protein | 259 | 42% helix, 17% strand | E0YCS2 |
Ligands and binding sites
- 2TD · tridec-12-en-2-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.77 | 0.90 | 36 | 2TD |
| 2 | 385 | 0.75 | 0.85 | 52 | 2TD |
| 3 | 111 | 0.37 | 0.74 | 25 | empty |
| 4 | 52 | 0.26 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 881 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3STW · Crystal Structure of tomato Methylketone Synthase I complexed with 2-trideca · 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 E0YCS2
- Elsewhere: RCSB PDB 3STW · PDBe 3STW · UniProt E0YCS2
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