Research workbench
The structure of chicken mitochondrial pepck in complex with pep
Analyse The structure of chicken mitochondrial pepck in complex with pep in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QZY
- Type
- protein
- Length
- 1,193 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase [GTP]
- EC
- 4.1.1.32
- UniProt
- P21642
- Ligands
- PEP, TQY, FRU, MN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32) | protein | 596 | 30% helix, 23% strand | P21642 |
| B | Phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32) | protein | 597 | 31% helix, 24% strand | P21642 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- TQY · 6-O-octanoyl-alpha-D-glucopyranose · ligand · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.78 | 0.80 | 88 | TQY, FRU |
| 2 | 86 | 0.77 | 0.98 | 19 | empty |
| 3 | 91 | 0.76 | 0.97 | 20 | empty |
| 4 | 487 | 0.70 | 0.80 | 54 | PEP |
| 5 | 534 | 0.70 | 0.79 | 62 | MN, PEP |
Interfaces
1 interface between chains.
- A–B · 588 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2QZY · The structure of chicken mitochondrial PEPCK in complex with PEP · the same entry in another collection · chain A against A, TM-score 1.00
- P21642 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase [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 P21642
- Elsewhere: RCSB PDB 2QZY · PDBe 2QZY · UniProt P21642
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