Research workbench
Epsps liganded with the (R)-phosphonate analog of the tetrahedral reaction intermediate
Analyse Epsps liganded with the (R)-phosphonate analog of the tetrahedral reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X8T
- 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
- RC1
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 427 | 36% helix, 25% strand | P0A6D3 |
Ligands and binding sites
- RC1 · [3R-[3A,4A,5B(R*)]]-5-(1-carboxy-1-phosphonoethoxy)-4-hydroxy-3-(phosphonooxy)-1-cyclohexene-1-carboxylic acid · ligand · chains A
- FMT · Formic acid · additive · 7 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 | 167 | 0.81 | 0.97 | 39 | RC1 |
| 2 | 62 | 0.32 | 0.76 | 14 | empty |
Compared structures
- 1X8T · EPSPS liganded with the (R)-phosphonate analog of the tetrahedral reaction intermediate · 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 1X8T · PDBe 1X8T · UniProt P0A6D3
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