Research workbench
E. COLI epsp synthase (T97I) liganded with S3P and glyphosate
Analyse E. COLI epsp synthase (T97I) liganded with S3P and glyphosate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FJZ
- Type
- protein
- Length
- 427 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoshikimate 1-carboxyvinyltransferase
- EC
- 2.5.1.19
- UniProt
- P0A6D3
- Ligands
- SER, GPF, S3P
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 427 | 36% helix, 27% strand | P0A6D3 |
Ligands and binding sites
- SER · Serine · ligand · chains A
- GPF · N-(phosphonomethyl)glycine · ligand · chains A
- S3P · Shikimate-3-phosphate · ligand · chains A
- FMT · Formic acid · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.76 | 0.98 | 28 | GPF, S3P |
| 2 | 75 | 0.33 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3FJZ · E. coli EPSP synthase (T97I) liganded with S3P and glyphosate · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6D3 · AlphaFold monomer V2.0 prediction for 3-phosphoshikimate 1-carboxyvinyltransferase… · 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 P0A6D3
- Elsewhere: RCSB PDB 3FJZ · PDBe 3FJZ · UniProt P0A6D3
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