Research workbench
Structure of rat cytosolic PEPCK Ld_1g in complex with PEP and GDP
Analyse Structure of rat cytosolic PEPCK Ld_1g in complex with PEP and GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GMW
- Type
- protein
- Length
- 611 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Rattus norvegicus
- Molecule
- Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
- EC
- 4.1.1.32
- UniProt
- P07379
- Ligands
- GDP, PEP, MN, NA
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.75 · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 611 | 30% helix, 23% strand | P07379 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- PEP · Phosphoenolpyruvate · ligand · chains A
- MN · Manganese (II) ion · metal · 4 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.67 | 0.79 | 55 | GDP, MN, PEP |
| 2 | 149 | 0.60 | 0.84 | 20 | empty |
| 3 | 84 | 0.46 | 0.80 | 20 | empty |
| 4 | 77 | 0.41 | 0.79 | 23 | empty |
| 5 | 59 | 0.34 | 0.78 | 18 | NA |
Compared structures
- 4GMW · Structure of rat cytosolic pepck LD_1G in complex with pep 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 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 P07379
- Elsewhere: RCSB PDB 4GMW · PDBe 4GMW · UniProt P07379
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