Research workbench
A100G CP4 epsps liganded with (R)-difluoromethyl tetrahedral reaction intermediate analog
Analyse A100G CP4 epsps liganded with (R)-difluoromethyl tetrahedral reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PQD
- Type
- protein
- Length
- 445 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
- Q9R4E4
- Ligands
- GG9
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 445 | 32% helix, 28% strand | Q9R4E4 |
Ligands and binding sites
- GG9 · (3R,4S,5R)-5-[(1R)-1-carboxy-2,2-difluoro-1-(phosphonooxy)ethoxy]-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid · ligand · 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 | 117 | 0.76 | 0.96 | 31 | GG9 |
| 2 | 88 | 0.45 | 0.80 | 17 | empty |
Compared structures
- 2PQD · A100G CP4 EPSPS liganded with (R)-difluoromethyl tetrahedral reaction intermediate analog · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R4E4 · 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 Q9R4E4
- Elsewhere: RCSB PDB 2PQD · PDBe 2PQD · UniProt Q9R4E4
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