MolNFT v1 · #147422 · protein
Pyruvate kinase isoform L-type with phosphorylated SER113 (PS113) in complex with fbp
6ECK · Pyruvate kinase pklr: “Pyruvate kinase isoform L-type with phosphorylated SER113 (PS113) in complex with fbp”. X-ray diffraction, 1 ligand (FBP), 17 pockets (best druggability 0.82). MolNFT v1 #147422 on GenesisL1: 3D structure…
- PDB
- 6ECK
- Type
- protein
- Length
- 1,061 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pklr
- EC
- 2.7.1.40
- UniProt
- P12928
- Ligands
- FBP
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 529 | 41% helix, 21% strand | P12928 |
| B | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 532 | 41% helix, 20% strand | P12928 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- FLC · Citrate anion · additive · chains B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.82 | 0.92 | 48 | PEG |
| 2 | 571 | 0.74 | 0.81 | 72 | GOL |
| 3 | 288 | 0.73 | 0.86 | 45 | empty |
| 4 | 52 | 0.70 | 0.97 | 25 | empty |
| 5 | 67 | 0.70 | 0.96 | 22 | GOL |
Interfaces
1 interface between chains.
- A–B · 1851 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6ECK · Pyruvate Kinase Isoform L-type with phosphorylated Ser113 (pS113) in complex with FBP · the same entry in another collection · chain A against A, TM-score 1.00
- P12928 · AlphaFold monomer V2.0 prediction for pyruvate kinase pklr (P12928) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P12928
- Elsewhere: RCSB PDB 6ECK · PDBe 6ECK · UniProt P12928
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