Research workbench
Structural studies of streptococcus pneumoniae epsp synthase in unliganded state
Analyse Structural studies of streptococcus pneumoniae epsp synthase in unliganded state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RF5
- 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
- Pockets
- 10 · best druggability 0.86
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 |
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.86 | 0.87 | 113 | empty |
| 2 | 1047 | 0.86 | 0.87 | 123 | empty |
| 3 | 1171 | 0.85 | 0.86 | 128 | empty |
| 4 | 877 | 0.84 | 0.86 | 105 | empty |
| 5 | 67 | 0.67 | 0.95 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1026 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 954 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 935 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 769 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1RF5 · Structural Studies of Streptococcus pneumoniae EPSP Synthase in Unliganded 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 0.87
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 1RF5 · PDBe 1RF5 · UniProt Q9S400
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