MolNFT v1 · #36594 · protein
The structure of mitochondrial pepck, complex with mn and GDP
2FAH · Phosphoenolpyruvate carboxykinase: “The structure of mitochondrial pepck, complex with mn and GDP”. X-ray diffraction, 4 ligands (GDP, TQY, FRU), 20 pockets (best druggability 0.81). MolNFT v1 #36594 on GenesisL1: 3D structure…
- PDB
- 2FAH
- Type
- protein
- Length
- 2,432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase
- EC
- 4.1.1.32
- UniProt
- P21642
- Ligands
- GDP, TQY, FRU, MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphoenolpyruvate carboxykinase (EC 4.1.1.32) | protein | 608 | 30% helix, 24% strand | P21642 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- TQY · 6-O-octanoyl-alpha-D-glucopyranose · ligand · 2 copies · chains C, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- MLA · Malonic acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.81 | 0.83 | 131 | GDP, MLA, MN |
| 2 | 1095 | 0.81 | 0.82 | 114 | empty |
| 3 | 822 | 0.81 | 0.84 | 96 | GDP, MLA, MN |
| 4 | 89 | 0.79 | 0.99 | 18 | empty |
| 5 | 86 | 0.78 | 0.99 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 753 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 694 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 664 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2FAH · The structure of mitochondrial PEPCK, Complex with Mn and GDP · 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 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 P21642
- Elsewhere: RCSB PDB 2FAH · PDBe 2FAH · UniProt P21642
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