MolNFT v1 · #20448 · protein
Structural studies of streptococcus pneumoniae epsp synthase, tetrahedral intermediate bound state
1RF4 · 5-enolpyruvylshikimate-3-phosphate synthase: “Structural studies of streptococcus pneumoniae epsp synthase, tetrahedral intermediate bound state”. X-ray diffraction, 1 ligand (SPQ), 12 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 1RF4
- 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
- SPQ
- Pockets
- 12 · 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
- SPQ · (3R,4S,5R)-5-{[(1R)-1-carboxy-2-fluoro-1-(phosphonooxy)ethyl]oxy}-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.80 | 0.81 | 90 | empty |
| 2 | 113 | 0.76 | 0.96 | 30 | SPQ |
| 3 | 555 | 0.74 | 0.81 | 53 | empty |
| 4 | 170 | 0.73 | 0.91 | 36 | SPQ |
| 5 | 162 | 0.72 | 0.91 | 37 | SPQ |
Interfaces
4 interfaces between chains.
- A–B · 411 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 384 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 273 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1RF4 · Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate… · 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 1RF4 · PDBe 1RF4 · UniProt Q9S400
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