Research workbench
Pyruvate kinase M2 mutant-N70D
Analyse Pyruvate kinase M2 mutant-N70D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L21
- Type
- protein
- Length
- 2,052 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
- OXL, FBP, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 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 | 515 | 39% helix, 21% strand | P14618 |
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 518 | 38% helix, 21% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 504 | 39% helix, 20% strand | P14618 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 copies · chains A, B, C, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.77 | 0.89 | 59 | empty |
| 2 | 520 | 0.73 | 0.81 | 59 | OXL, MG, GOL |
| 3 | 581 | 0.72 | 0.80 | 65 | OXL, MG, GOL |
| 4 | 544 | 0.71 | 0.80 | 59 | OXL, MG, GOL |
| 5 | 506 | 0.71 | 0.80 | 55 | OXL, MG, GOL |
Interfaces
5 interfaces between chains.
- B–C · 470 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 244 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 200 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 83 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7L21 · Pyruvate Kinase M2 mutant-N70D · 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 7L21 · PDBe 7L21 · UniProt P14618
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