Research workbench
E. COLI phosphoenolpyruvate carboxykinase (pepck) complexed with ATP, MG2+, MN2+, carbon dioxide and oxaloacetate
Analyse E. COLI phosphoenolpyruvate carboxykinase (pepck) complexed with ATP, MG2+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PXZ
- Type
- protein
- Length
- 526 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase
- EC
- 4.1.1.49
- UniProt
- P22259
- Ligands
- OAA, ATP, MG, MN, CO2
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Phosphoenolpyruvate carboxykinase (EC 4.1.1.49) | protein | 526 | 30% helix, 25% strand | P22259 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · chains X
- ATP · Adenosine-5'-triphosphate · ligand · chains X
- MG · Magnesium ion · metal · chains X
- MN · Manganese (II) ion · metal · chains X
- CO2 · Carbon dioxide · ion · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.69 | 0.80 | 67 | MG, MN, OAA, ATP, CO2 |
| 2 | 112 | 0.42 | 0.77 | 21 | empty |
| 3 | 75 | 0.35 | 0.76 | 20 | empty |
Compared structures
- 2PXZ · E. coli phosphoenolpyruvate carboxykinase (PEPCK) complexed with ATP, Mg2+, Mn2+, carbon… · the same entry in another collection · chain X against X, TM-score 1.00
- P22259 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase (ATP) (P22259) · a predicted model of the same protein · chain X against A, TM-score 0.95
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 P22259
- Elsewhere: RCSB PDB 2PXZ · PDBe 2PXZ · UniProt P22259
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