MolNFT v1 · #54773 · protein
Crystal structure from the phosphoenolpyruvate-binding domain of enzyme I in complex with pyruvate from the thermoanaerobacter tengcongensis pep-sugar phosphotransferase system (pts)
2XZ9 · Phosphoenolpyruvate-protein kinase (pts system ei component…: “Crystal structure from the phosphoenolpyruvate-binding domain of enzyme I in complex with pyruvate from the…”. X-ray diffraction, 2 ligands (PYR, MG), 6 pockets (best…
- PDB
- 2XZ9
- Type
- protein
- Length
- 633 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate-protein kinase (pts system ei component in bacteria)
- EC
- 2.7.3.9
- UniProt
- Q8R7R4
- Ligands
- PYR, MG
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate-protein kinase (pts system ei component in bacteria) (EC 2.7.3.9) | protein | 317 | 52% helix, 14% strand | Q8R7R4 |
| B | Phosphoenolpyruvate-protein kinase (pts system ei component in bacteria) (EC 2.7.3.9) | protein | 316 | 51% helix, 13% strand | Q8R7R4 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.55 | 0.78 | 30 | MG, PYR |
| 2 | 224 | 0.53 | 0.77 | 31 | MG, PYR |
| 3 | 118 | 0.46 | 0.79 | 15 | empty |
| 4 | 92 | 0.46 | 0.80 | 21 | empty |
| 5 | 68 | 0.38 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2033 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2XZ9 · Crystal structure from the phosphoenolpyruvate-binding domain of enzyme I in complex with… · the same entry in another collection · chain A 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 Q8R7R4
- Elsewhere: RCSB PDB 2XZ9 · PDBe 2XZ9 · UniProt Q8R7R4
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