Research workbench
Resolving the activation site of positive regulators in plant phosphoenolpyruvate carboxylase
Analyse Resolving the activation site of positive regulators in plant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BXC
- Type
- protein
- Length
- 1,858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.86
- Source
- Flaveria trinervia
- Molecule
- C4 phosphoenolpyruvate carboxylase
- EC
- 4.1.1.31
- UniProt
- P30694
- Ligands
- G6P, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.86 · 2 distinct chains · 65% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C4 phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 929 | 65% helix, 6% strand | P30694 |
| B | C4 phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 929 | 65% helix, 6% strand | P30694 |
Ligands and binding sites
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.86 | 0.87 | 120 | G6P |
| 2 | 562 | 0.82 | 0.87 | 52 | empty |
| 3 | 239 | 0.81 | 0.94 | 32 | empty |
| 4 | 880 | 0.80 | 0.83 | 95 | empty |
| 5 | 510 | 0.79 | 0.86 | 60 | G6P |
Interfaces
1 interface between chains.
- A–B · 599 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4BXC · Resolving the activation site of positive regulators in plant phosphoenolpyruvate… · the same entry in another collection · chain A against A, TM-score 1.00
- P30694 · AlphaFold monomer V2.0 prediction for C4 phosphoenolpyruvate carboxylase (P30694) · a predicted model of the same protein · chain A 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 P30694
- Elsewhere: RCSB PDB 4BXC · PDBe 4BXC · UniProt P30694
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