MolNFT v1 · #18308 · protein
Structure of rabbit muscle pyruvate kinase complexed with MN2+, K+, and pyruvate
1PKN: “Structure of rabbit muscle pyruvate kinase complexed with MN2+, K+, and pyruvate”. X-ray diffraction, 3 ligands (PYR, K, MN), 8 pockets (best druggability 0.74). MolNFT v1 #18308 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1PKN
- Type
- protein
- Length
- 514 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- P11974
- Ligands
- PYR, K, MN
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 514 | 39% helix, 19% strand | P11974 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains A
- K · Potassium ion · metal · chains A
- MN · Manganese (II) 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.74 | 0.81 | 57 | K, MN, PYR |
| 2 | 184 | 0.62 | 0.83 | 28 | empty |
| 3 | 216 | 0.47 | 0.74 | 32 | empty |
| 4 | 100 | 0.43 | 0.78 | 21 | empty |
| 5 | 62 | 0.34 | 0.77 | 19 | empty |
Compared structures
- 1PKN · Structure of rabbit muscle pyruvate kinase complexed with MN2+, K+, and pyruvate · the same entry in another collection · chain A against A, TM-score 1.00
- P11974 · AlphaFold monomer V2.0 prediction for pyruvate kinase pkm (P11974) · 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 P11974
- Elsewhere: RCSB PDB 1PKN · PDBe 1PKN · UniProt P11974
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