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The structure of human liver pyruvate kinase, hlpyk-D499N, in complex with fru-1,6-bp
Analyse The structure of human liver pyruvate kinase, hlpyk-D499N, in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NN4
- Type
- protein
- Length
- 1,665 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pklr
- EC
- 2.7.1.40
- UniProt
- P30613
- Ligands
- FBP, PEP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 418 | 48% helix, 17% strand | P30613 |
| B | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 414 | 48% helix, 18% strand | P30613 |
| C | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 419 | 49% helix, 17% strand | P30613 |
| D | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 414 | 49% helix, 17% strand | P30613 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.86 | 0.96 | 57 | empty |
| 2 | 334 | 0.86 | 0.95 | 42 | empty |
| 3 | 531 | 0.85 | 0.91 | 38 | empty |
| 4 | 537 | 0.79 | 0.86 | 69 | EDO |
| 5 | 455 | 0.79 | 0.87 | 57 | EDO |
Interfaces
6 interfaces between chains.
- A–C · 2620 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 2618 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1649 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1603 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NN4 · The structure of human liver pyruvate kinase, hLPYK-D499N, in complex with Fru-1,6-BP · 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 P30613
- Elsewhere: RCSB PDB 6NN4 · PDBe 6NN4 · UniProt P30613
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