Research workbench
The structure of rat cytosolic pepck in complex with phosphoglycolate and GDP
Analyse The structure of rat cytosolic pepck in complex with phosphoglycolate and GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DTB
- Type
- protein
- Length
- 1,232 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
- EC
- 4.1.1.32
- UniProt
- P07379
- Ligands
- PGA, GDP, BCT, MN, NA
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 620 | 30% helix, 23% strand | P07379 |
| B | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 612 | 31% helix, 23% strand | P07379 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · chains A
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.80 | 0.82 | 90 | empty |
| 2 | 467 | 0.71 | 0.81 | 61 | PGA, MN, GDP |
| 3 | 380 | 0.70 | 0.82 | 55 | PGA, MN, GDP |
| 4 | 151 | 0.60 | 0.83 | 20 | empty |
| 5 | 156 | 0.60 | 0.83 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 477 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3DTB · The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP · the same entry in another collection · chain A against A, TM-score 1.00
- P07379 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase, cytosolic [GTP]… · a predicted model of the same protein · 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 P07379
- Elsewhere: RCSB PDB 3DTB · PDBe 3DTB · UniProt P07379
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