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The structure of rat cytosolic pepck variant E89Q in complex with phosphoglycolate and GDP
Analyse The structure of rat cytosolic pepck variant E89Q in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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