MolNFT v1 · #92935 · protein
Structure of rat cytosolic pepck LD_2G in complex with pep and GDP
4GNL · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “Structure of rat cytosolic pepck LD_2G in complex with pep and GDP”. X-ray diffraction, 4 ligands (GDP, PEP, MN), 7 pockets (best druggability 0.68). MolNFT v1 #92935 on…
- PDB
- 4GNL
- Type
- protein
- Length
- 604 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, PEP, MN, NA
- Pockets
- 7 · best druggability 0.68
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 | 604 | 31% 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 · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.68 | 0.79 | 53 | MN, GDP, PEP |
| 2 | 160 | 0.60 | 0.83 | 20 | empty |
| 3 | 88 | 0.50 | 0.82 | 19 | empty |
| 4 | 84 | 0.43 | 0.80 | 24 | empty |
| 5 | 55 | 0.33 | 0.78 | 18 | NA |
Compared structures
- 4GNL · Structure of rat cytosolic PEPCK Ld_2g 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 4GNL · PDBe 4GNL · UniProt P07379
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