MolNFT v1 · #176896 · protein
Caprylic acid targets a serine hydroxymethyltransferase to kill horseweed
7E13: “Caprylic acid targets a serine hydroxymethyltransferase to kill horseweed”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.75). MolNFT v1 #176896 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E13
- Type
- protein
- Length
- 1,900 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Serine hydroxymethyltransferase | protein | 475 | 47% helix, 14% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.75 | 0.83 | 71 | PLP |
| 2 | 1000 | 0.75 | 0.78 | 92 | empty |
| 3 | 933 | 0.74 | 0.78 | 75 | empty |
| 4 | 382 | 0.73 | 0.84 | 37 | empty |
| 5 | 431 | 0.73 | 0.83 | 50 | PLP |
Interfaces
6 interfaces between chains.
- A–B · 5185 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 5020 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 990 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 894 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7E13 · Caprylic acid targets a serine hydroxymethyltransferase to kill horseweed · 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
- Elsewhere: RCSB PDB 7E13 · PDBe 7E13
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.