Research workbench
Crystal structure of phosphoenolpyruvate carboxylase from arabidopsis thaliana in complex with aspartate and citrate
Analyse Crystal structure of phosphoenolpyruvate carboxylase from arabidopsis thaliana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FDN
- Type
- protein
- Length
- 1,814 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxylase 3
- EC
- 4.1.1.31
- UniProt
- Q84VW9
- Ligands
- ASP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxylase 3 (EC 4.1.1.31) | protein | 914 | 66% helix, 5% strand | Q84VW9 |
| B | Phosphoenolpyruvate carboxylase 3 (EC 4.1.1.31) | protein | 900 | 66% helix, 6% strand | Q84VW9 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, B
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 | 1110 | 0.86 | 0.87 | 102 | empty |
| 2 | 164 | 0.78 | 0.95 | 31 | ASP, FLC |
| 3 | 157 | 0.77 | 0.94 | 29 | ASP, FLC |
| 4 | 340 | 0.74 | 0.85 | 46 | empty |
| 5 | 370 | 0.73 | 0.84 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 646 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5FDN · Crystal structure of phosphoenolpyruvate carboxylase from Arabidopsis thaliana in complex… · the same entry in another collection · chain B against B, TM-score 1.00
- Q84VW9 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxylase 3 (Q84VW9) · a predicted model of the same protein · chain B 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 Q84VW9
- Elsewhere: RCSB PDB 5FDN · PDBe 5FDN · UniProt Q84VW9
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