MolNFT v1 · #20450 · protein
Structural studies of streptococcus pneumoniae epsp synthase in S3P-glp bound state
1RF6 · 5-enolpyruvylshikimate-3-phosphate synthase: “Structural studies of streptococcus pneumoniae epsp synthase in S3P-glp bound state”. X-ray diffraction, 2 ligands (GPJ, S3P), 11 pockets (best druggability 0.80). MolNFT v1 #20450 on…
- PDB
- 1RF6
- Type
- protein
- Length
- 1,708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-enolpyruvylshikimate-3-phosphate synthase
- EC
- 2.5.1.19
- UniProt
- Q9S400
- Ligands
- GPJ, S3P
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) | protein | 427 | 34% helix, 27% strand | Q9S400 |
Ligands and binding sites
- GPJ · Glyphosate · ligand · 4 copies · chains A, B, C, D
- S3P · Shikimate-3-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.80 | 0.82 | 105 | empty |
| 2 | 142 | 0.74 | 0.93 | 32 | GPJ, S3P |
| 3 | 770 | 0.74 | 0.79 | 61 | empty |
| 4 | 661 | 0.73 | 0.80 | 67 | empty |
| 5 | 182 | 0.72 | 0.90 | 38 | GPJ, S3P |
Interfaces
4 interfaces between chains.
- A–B · 433 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 410 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 283 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 278 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1RF6 · Structural Studies of Streptococcus pneumoniae EPSP Synthase in S3P-GLP Bound State · the same entry in another collection · chain D against D, TM-score 1.00
- Q9S400 · AlphaFold monomer V2.0 prediction for 3-phosphoshikimate 1-carboxyvinyltransferase… · a predicted model of the same protein · chain D 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 Q9S400
- Elsewhere: RCSB PDB 1RF6 · PDBe 1RF6 · UniProt Q9S400
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