MolNFT v1 · #12455 · protein
Pepck complex with nonhydrolyzable GTP analog, native data
1KHB · Phosphoenolpyruvate carboxykinase, cytosolic (GTP): “Pepck complex with nonhydrolyzable GTP analog, native data”. X-ray diffraction, 2 ligands (GCP, MN), 7 pockets (best druggability 0.69). MolNFT v1 #12455 on GenesisL1: 3D…
- PDB
- 1KHB
- 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 0.69
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
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 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 | 390 | 0.69 | 0.81 | 55 | MN, ACT, GCP |
| 2 | 156 | 0.56 | 0.81 | 21 | empty |
| 3 | 74 | 0.48 | 0.84 | 19 | empty |
| 4 | 116 | 0.45 | 0.78 | 26 | empty |
| 5 | 54 | 0.35 | 0.78 | 15 | empty |
Compared structures
- 1KHB · PEPCK complex with nonhydrolyzable GTP analog, native 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 1KHB · PDBe 1KHB · UniProt P35558
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.