Research workbench
Structure of liver pyruvate kinase in complex with allosteric modulator 3
Analyse Structure of liver pyruvate kinase in complex with allosteric modulator 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FRV
- Type
- protein
- Length
- 3,405 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.004
- Source
- Homo sapiens
- Molecule
- Pyruvate kinase PKLR
- EC
- 2.7.1.40
- UniProt
- P30613
- Ligands
- OXL, OD5, FBP, MG, K
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.004 · 7 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase PKLR (EC 2.7.1.40) | protein | 422 | 47% helix, 17% strand | P30613 |
| B | Pyruvate kinase PKLR (EC 2.7.1.40) | protein | 436 | 49% helix, 16% strand | P30613 |
| C | Pyruvate kinase PKLR (EC 2.7.1.40) | protein | 425 | 47% helix, 17% strand | P30613 |
| D, H | Pyruvate kinase PKLR (EC 2.7.1.40) | protein | 425 | 47% helix, 17% strand | P30613 |
| E | Pyruvate kinase PKLR (EC 2.7.1.40) | protein | 419 | 47% helix, 17% strand | P30613 |
| F | Pyruvate kinase PKLR (EC 2.7.1.40) | protein | 432 | 50% helix, 16% strand | P30613 |
| G | Pyruvate kinase PKLR (EC 2.7.1.40) | protein | 421 | 47% helix, 17% strand | P30613 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- OD5 · 4,4'-sulfonyldi(benzene-1,2-diol) · ligand · 4 copies · chains A, C, B, D, F, H, E, G
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · sugar · 8 copies · chains A, B, C, G, D, E, F, H
- MG · Magnesium 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
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 | 421 | 0.87 | 0.95 | 56 | OD5 |
| 2 | 408 | 0.87 | 0.95 | 49 | OD5 |
| 3 | 401 | 0.87 | 0.95 | 46 | OD5 |
| 4 | 403 | 0.87 | 0.94 | 46 | OD5 |
| 5 | 838 | 0.87 | 0.89 | 60 | empty |
Interfaces
13 interfaces between chains.
- B–D · 2643 Ų buried · 40 hydrogen bonds · protein-protein
- E–G · 2625 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 2622 Ų buried · 40 hydrogen bonds · protein-protein
- F–H · 2620 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 1673 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- P30613 · AlphaFold monomer V2.0 prediction for pyruvate kinase pklr (P30613) · 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 P30613
- Elsewhere: RCSB PDB 7FRV · PDBe 7FRV · UniProt P30613
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