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The location of the allosteric amino acid binding site of muscle pyruvate kinase.
Analyse The location of the allosteric amino acid binding site of muscle pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G50
- Type
- protein
- Length
- 4,128 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase isozymes M1/M2
- EC
- 2.7.1.40
- UniProt
- P11974
- Ligands
- ALA, PYR, ETE, NA, MN, K
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 519 | 39% helix, 21% strand | P11974 |
| B | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 511 | 40% helix, 20% strand | P11974 |
| C | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 512 | 40% helix, 20% strand | P11974 |
| D, E | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 521 | 39% helix, 21% strand | P11974 |
| F | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 515 | 40% helix, 21% strand | P11974 |
| G | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 510 | 39% helix, 20% strand | P11974 |
| H | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 519 | 39% helix, 21% strand | P11974 |
Ligands and binding sites
- ALA · Alanine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PYR · Pyruvic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · chains B
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 29 copies · chains A, C, B, D, E, F, H, G
- GOL · Glycerol · additive · 28 copies · chains A, B, C, D, E, F, H, G
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 | 1079 | 0.89 | 0.91 | 98 | empty |
| 2 | 452 | 0.88 | 0.95 | 38 | empty |
| 3 | 445 | 0.87 | 0.94 | 37 | empty |
| 4 | 396 | 0.87 | 0.95 | 39 | empty |
| 5 | 396 | 0.87 | 0.95 | 43 | empty |
Interfaces
14 interfaces between chains.
- F–H · 2987 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2942 Ų buried · 31 hydrogen bonds · protein-protein
- E–G · 2916 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2889 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1440 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2G50 · The location of the allosteric amino acid binding site of muscle pyruvate kinase. · the same entry in another collection · chain E against E, TM-score 1.00
- P11974 · AlphaFold monomer V2.0 prediction for pyruvate kinase pkm (P11974) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 P11974
- Elsewhere: RCSB PDB 2G50 · PDBe 2G50 · UniProt P11974
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