MolNFT v1 · #118938 · protein
The structure of rat cytosolic pepck variant E89Q in complex with phosphoglycolate and GDP
5FH5 · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “The structure of rat cytosolic pepck variant E89Q in complex with phosphoglycolate and GDP”. X-ray diffraction, 4 ligands (GDP, PGA, MN), 8 pockets (best druggability 0.74).…
- PDB
- 5FH5
- Type
- protein
- Length
- 610 residues
- Chains
- 1
- 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
- GDP, PGA, MN, NA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 610 | 31% helix, 23% strand | P07379 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- PGA · 2-phosphoglycolic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.74 | 0.81 | 69 | MN, GDP, PGA |
| 2 | 166 | 0.61 | 0.83 | 20 | empty |
| 3 | 92 | 0.48 | 0.81 | 17 | empty |
| 4 | 69 | 0.39 | 0.79 | 25 | empty |
| 5 | 93 | 0.36 | 0.75 | 21 | empty |
Compared structures
- 5FH5 · The structure of rat cytosolic PEPCK variant E89Q in complex with phosphoglycolate and GDP · 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 P07379
- Elsewhere: RCSB PDB 5FH5 · PDBe 5FH5 · UniProt P07379
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.