Research workbench
Crystal structure of human pyruvate kinase M2 isoform
Analyse Crystal structure of human pyruvate kinase M2 isoform in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JFB
- Type
- protein
- Length
- 2,082 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pkm isoform M2
- EC
- 2.7.1.40
- UniProt
- P14618
- Ligands
- SER, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pkm isoform M2 (EC 2.7.1.40) | protein | 522 | 38% helix, 19% strand | P14618 |
| B | Pyruvate kinase pkm isoform M2 (EC 2.7.1.40) | protein | 521 | 36% helix, 20% strand | P14618 |
| C | Pyruvate kinase pkm isoform M2 (EC 2.7.1.40) | protein | 523 | 37% helix, 20% strand | P14618 |
| D | Pyruvate kinase pkm isoform M2 (EC 2.7.1.40) | protein | 516 | 39% helix, 20% strand | P14618 |
Ligands and binding sites
- SER · Serine · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
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 | 369 | 0.86 | 0.95 | 43 | empty |
| 2 | 360 | 0.85 | 0.94 | 42 | empty |
| 3 | 68 | 0.74 | 0.99 | 29 | SER |
| 4 | 61 | 0.72 | 0.99 | 26 | SER |
| 5 | 63 | 0.72 | 0.98 | 27 | SER |
Interfaces
4 interfaces between chains.
- C–D · 2514 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2485 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1314 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1293 Ų buried · 9 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 6JFB · PDBe 6JFB · UniProt P14618
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