MolNFT v1 · #12458 · protein
Pepck complex with nonhydrolyzable GTP analog, mad data
1KHE · Phosphoenolpyruvate carboxykinase, cytosolic (GTP): “Pepck complex with nonhydrolyzable GTP analog, mad data”. X-ray diffraction, 2 ligands (GCP, MN), 7 pockets (best druggability 0.70). MolNFT v1 #12458 on GenesisL1: 3D structure…
- PDB
- 1KHE
- Type
- protein
- Length
- 603 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
- P35558
- Ligands
- GCP, MN
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic (GTP) (EC 4.1.1.32) | protein | 603 | 32% helix, 24% strand | P35558 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.70 | 0.82 | 55 | MN, GCP |
| 2 | 143 | 0.56 | 0.81 | 21 | empty |
| 3 | 63 | 0.46 | 0.83 | 16 | empty |
| 4 | 101 | 0.42 | 0.78 | 22 | empty |
| 5 | 61 | 0.36 | 0.78 | 19 | empty |
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 1KHE · PEPCK complex with nonhydrolyzable GTP analog, MAD data · the same entry in another collection · chain A against A, TM-score 1.00
- P35558 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase, cytosolic [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 P35558
- Elsewhere: RCSB PDB 1KHE · PDBe 1KHE · UniProt P35558
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