MolNFT v1 · #166978 · protein
Crystal structure of human PKM2 in complex with L-valine
6V76 · Pyruvate kinase pkm: “Crystal structure of human PKM2 in complex with L-valine”. X-ray diffraction, 6 ligands (FBP, OXL, VAL), 20 pockets (best druggability 0.85). MolNFT v1 #166978 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6V76
- Type
- protein
- Length
- 1,968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pkm
- EC
- 2.7.1.40
- UniProt
- P14618
- Ligands
- FBP, OXL, VAL, MG, K, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 511 | 39% helix, 20% strand | P14618 |
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 515 | 39% helix, 20% strand | P14618 |
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 511 | 39% helix, 19% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 431 | 45% helix, 16% strand | P14618 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains C, A, B, D
- OXL · Oxalate ion · ligand · 2 copies · chains C, B
- VAL · Valine · ligand · 2 copies · chains C, B
- MG · Magnesium ion · metal · 2 copies · chains C, B
- K · Potassium ion · metal · chains C
- CL · Chloride ion · ion · 2 copies · chains C, A
- GOL · Glycerol · additive · 12 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.85 | 0.94 | 42 | empty |
| 2 | 981 | 0.82 | 0.83 | 135 | MG, OXL |
| 3 | 773 | 0.75 | 0.79 | 82 | CL, K, MG, GOL, OXL |
| 4 | 103 | 0.72 | 0.94 | 35 | empty |
| 5 | 610 | 0.71 | 0.79 | 70 | CL |
Interfaces
5 interfaces between chains.
- C–B · 2593 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 208 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 201 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 158 Ų buried · 0 hydrogen bonds · protein-protein
- C–A · 126 Ų buried · 0 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 6V76 · PDBe 6V76 · UniProt P14618
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