MolNFT v1 · #50512 · protein
The structure of rat cytosolic pepck in complex with sulfoacetate.
2RKE · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “The structure of rat cytosolic pepck in complex with sulfoacetate.”. X-ray diffraction, 4 ligands (SAT, MN, NA), 9 pockets (best druggability 0.71). MolNFT v1 #50512 on GenesisL1…
- PDB
- 2RKE
- Type
- protein
- Length
- 612 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
- SAT, MN, NA, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 612 | 30% helix, 24% strand | P07379 |
Ligands and binding sites
- SAT · sulfoacetic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.71 | 0.81 | 56 | SO4, SAT |
| 2 | 155 | 0.58 | 0.82 | 20 | empty |
| 3 | 78 | 0.48 | 0.82 | 16 | empty |
| 4 | 84 | 0.36 | 0.76 | 24 | empty |
| 5 | 64 | 0.35 | 0.77 | 15 | empty |
Compared structures
- 2RKE · The Structure of rat cytosolic PEPCK in complex with sulfoacetate. · 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 2RKE · PDBe 2RKE · UniProt P07379
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