MolNFT v1 · #11995 · protein
Phosphoenolpyruvate carboxykinase in complex with ADP, ALF3 and pyruvate
1K3C: “Phosphoenolpyruvate carboxykinase in complex with ADP, ALF3 and pyruvate”. X-ray diffraction, 4 ligands (ADP, AF3, PYR), 3 pockets (best druggability 0.71). MolNFT v1 #11995 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1K3C
- Type
- protein
- Length
- 535 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase
- EC
- 4.1.1.49
- UniProt
- P22259
- Ligands
- ADP, AF3, PYR, MG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase (EC 4.1.1.49) | protein | 535 | 32% helix, 24% strand | P22259 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- AF3 · Aluminum fluoride · ligand · chains A
- PYR · Pyruvic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.71 | 0.79 | 68 | MG, ADP, AF3, PYR |
| 2 | 97 | 0.39 | 0.76 | 21 | empty |
| 3 | 51 | 0.29 | 0.75 | 14 | empty |
Compared structures
- 1K3C · Phosphoenolpyruvate carboxykinase in complex with ADP, AlF3 and Pyruvate · the same entry in another collection · chain A against A, TM-score 1.00
- P22259 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase (ATP) (P22259) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P22259
- Elsewhere: RCSB PDB 1K3C · PDBe 1K3C · UniProt P22259
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