Research workbench
Rat cytosolic pepck in complex with oxaloacetic acid.
Analyse Rat cytosolic pepck in complex with oxaloacetic acid. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QF1
- Type
- protein
- Length
- 606 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
- OAA, MN, NA
- Pockets
- 8 · best druggability 0.70
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 | 606 | 30% helix, 24% strand | P07379 |
Ligands and binding sites
- OAA · Oxaloacetate ion · 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.70 | 0.80 | 52 | MN, OAA |
| 2 | 145 | 0.58 | 0.83 | 20 | empty |
| 3 | 51 | 0.53 | 0.89 | 15 | empty |
| 4 | 62 | 0.42 | 0.80 | 22 | empty |
| 5 | 78 | 0.37 | 0.77 | 18 | empty |
Compared structures
- 2QF1 · Rat cytosolic PEPCK in complex with oxaloacetic acid. · 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 2QF1 · PDBe 2QF1 · UniProt P07379
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