Research workbench
2.50 ångström resolution structure of 3-phosphoshikimate 1- carboxyvinyltransferase (aroa) from coxiella burnetii in complex with phosphoenolpyruvate
Analyse 2.50 ångström resolution structure of 3-phosphoshikimate 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EGR
- Type
- protein
- Length
- 2,604 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoshikimate 1-carboxyvinyltransferase
- EC
- 2.5.1.19
- UniProt
- Q83E11
- Ligands
- PEP, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 434 | 35% helix, 26% strand | Q83E11 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.76 | 0.91 | 35 | SO4, PEP |
| 2 | 217 | 0.75 | 0.90 | 38 | SO4, PEP |
| 3 | 220 | 0.74 | 0.89 | 39 | SO4, PEP |
| 4 | 203 | 0.73 | 0.90 | 35 | SO4, PEP |
| 5 | 263 | 0.73 | 0.87 | 45 | PEP, SO4 |
Interfaces
7 interfaces between chains.
- A–B · 626 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 624 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 377 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 373 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4EGR · 2.50 angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase (AroA)… · the same entry in another collection · chain F against F, TM-score 1.00
- Q83E11 · AlphaFold monomer V2.0 prediction for 3-phosphoshikimate 1-carboxyvinyltransferase… · a predicted model of the same protein · chain C 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 Q83E11
- Elsewhere: RCSB PDB 4EGR · PDBe 4EGR · UniProt Q83E11
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