Research workbench
I45T cytosolic phosphoenolpyruvate carboxykinase in complex with beta-sulfopyruvate and GTP
Analyse I45T cytosolic phosphoenolpyruvate carboxykinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OX2
- Type
- protein
- Length
- 1,228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Rattus norvegicus
- Molecule
- Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
- EC
- 4.1.1.32
- UniProt
- P07379
- Ligands
- GTP, SPV, ETX, MN, NA
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 608 | 31% helix, 24% strand | P07379 |
| B | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 620 | 30% helix, 23% strand | P07379 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- SPV · Sulfopyruvate · ligand · 2 copies · chains A, B
- ETX · 2-ethoxyethanol · ligand · chains B
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.70 | 0.83 | 50 | MN, GTP, SPV |
| 2 | 391 | 0.69 | 0.81 | 53 | MN, GTP, SPV |
| 3 | 768 | 0.66 | 0.74 | 73 | empty |
| 4 | 148 | 0.57 | 0.82 | 20 | empty |
| 5 | 150 | 0.56 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 861 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4OX2 · I45T cytosolic phosphoenolpyruvate carboxykinase in complex with beta- sulfopyruvate and… · 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 B 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 4OX2 · PDBe 4OX2 · UniProt P07379
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