MolNFT v1 · #158447 · protein
Pyruvate kinase M2 mutant - S437Y in complex with L-cysteine
6NU5 · Pyruvate kinase pkm: “Pyruvate kinase M2 mutant - S437Y in complex with L-cysteine”. X-ray diffraction, 5 ligands (CYS, OXL, MG), 15 pockets (best druggability 0.87). MolNFT v1 #158447 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NU5
- Type
- protein
- Length
- 1,040 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
- CYS, OXL, MG, K, SCN
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% 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 | 518 | 39% helix, 21% strand | P14618 |
Ligands and binding sites
- CYS · Cysteine · ligand · 2 copies · chains A, B
- 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 · 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
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A
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 | 353 | 0.87 | 0.96 | 46 | EDO |
| 2 | 738 | 0.76 | 0.81 | 95 | OXL, B3P, MG |
| 3 | 539 | 0.75 | 0.83 | 60 | OXL, B3P, MG, K |
| 4 | 151 | 0.56 | 0.82 | 26 | CYS |
| 5 | 166 | 0.56 | 0.81 | 28 | CYS |
Interfaces
1 interface between chains.
- A–B · 2977 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
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 6NU5 · PDBe 6NU5 · UniProt P14618
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