MolNFT v1 · #61703 · protein
The structure of rat cytosolic pepck in complex with phosphoglycolate and GDP
3DTB · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “The structure of rat cytosolic pepck in complex with phosphoglycolate and GDP”. X-ray diffraction, 5 ligands (PGA, GDP, BCT), 18 pockets (best druggability 0.80). MolNFT v1 #61703…
- 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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