MolNFT v1 · #143684 · protein
Pyruvate kinase M2 mutant - S437Y
6B6U · Pyruvate kinase pkm: “Pyruvate kinase M2 mutant - S437Y”. X-ray diffraction, 5 ligands (OXL, MG, K), 15 pockets (best druggability 0.87). MolNFT v1 #143684 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6B6U
- Type
- protein
- Length
- 1,041 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pkm
- EC
- 2.7.1.40
- UniProt
- P14618
- Ligands
- OXL, MG, K, SCN, CL
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 522 | 39% helix, 20% strand | P14618 |
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 519 | 39% helix, 21% strand | P14618 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.87 | 0.96 | 56 | PG4, EDO |
| 2 | 476 | 0.76 | 0.85 | 61 | MG, OXL, B3P |
| 3 | 457 | 0.74 | 0.84 | 62 | MG, OXL, K, B3P |
| 4 | 131 | 0.59 | 0.84 | 23 | CL |
| 5 | 165 | 0.55 | 0.81 | 28 | CL |
Interfaces
1 interface between chains.
- A–B · 2958 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6B6U · Pyruvate Kinase M2 mutant - S437Y · the same entry in another collection · 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 P14618
- Elsewhere: RCSB PDB 6B6U · PDBe 6B6U · UniProt P14618
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