MolNFT v1 · #147419 · protein
Pyruvate kinase isoform L-type with phosphorylated SER12 (PS12) in complex with fbp
6ECH · Pyruvate kinase pklr: “Pyruvate kinase isoform L-type with phosphorylated SER12 (PS12) in complex with fbp”. X-ray diffraction, 5 ligands (FBP, OXL, ATP), 20 pockets (best druggability 0.86). MolNFT v1 #147419 on GenesisL1: 3D…
- PDB
- 6ECH
- Type
- protein
- Length
- 2,108 residues
- Chains
- 4
- 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, OXL, ATP, MG, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 528 | 40% helix, 22% strand | P12928 |
| B | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 525 | 40% helix, 22% strand | P12928 |
| C | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 528 | 41% helix, 21% strand | P12928 |
| D | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 527 | 40% helix, 21% strand | P12928 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, D
- MG · Magnesium ion · metal · 13 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C, D
- EDO · 1,2-ethanediol · additive · 33 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
- PG4 · Tetraethylene glycol · additive · chains A, C
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.86 | 0.87 | 144 | MG, ATP, OXL, EDO, PGE |
| 2 | 343 | 0.86 | 0.95 | 45 | empty |
| 3 | 347 | 0.86 | 0.95 | 45 | empty |
| 4 | 720 | 0.84 | 0.88 | 47 | empty |
| 5 | 437 | 0.80 | 0.88 | 59 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2874 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2867 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 1643 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1634 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ECH · Pyruvate Kinase Isoform L-type with phosphorylated Ser12 (pS12) in complex with FBP · the same entry in another collection · chain D against D, TM-score 1.00
- P12928 · AlphaFold monomer V2.0 prediction for pyruvate kinase pklr (P12928) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 6ECH · PDBe 6ECH · UniProt P12928
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