Research workbench
The structure of human liver pyruvate kinase, hlpyk-S531E
Analyse The structure of human liver pyruvate kinase, hlpyk-S531E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NN8
- Type
- protein
- Length
- 3,671 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pklr
- EC
- 2.7.1.40
- UniProt
- P30613
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 505 | 41% helix, 21% strand | P30613 |
| B | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 518 | 40% helix, 21% strand | P30613 |
| C | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 499 | 44% helix, 21% strand | P30613 |
| D | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 421 | 49% helix, 18% strand | P30613 |
| E | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 509 | 40% helix, 21% strand | P30613 |
| F | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 417 | 48% helix, 17% strand | P30613 |
| G | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 395 | 46% helix, 17% strand | P30613 |
| H | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 407 | 47% helix, 16% strand | P30613 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 41 copies · chains A, D, B, C, 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 | 1024 | 0.88 | 0.89 | 105 | EDO |
| 2 | 379 | 0.86 | 0.95 | 49 | empty |
| 3 | 340 | 0.86 | 0.95 | 42 | empty |
| 4 | 362 | 0.86 | 0.95 | 46 | empty |
| 5 | 331 | 0.86 | 0.95 | 45 | empty |
Interfaces
15 interfaces between chains.
- C–E · 2889 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2780 Ų buried · 47 hydrogen bonds · protein-protein
- D–H · 2672 Ų buried · 40 hydrogen bonds · protein-protein
- F–G · 2660 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 1750 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6NN8 · The structure of human liver pyruvate kinase, hLPYK-S531E · 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 6NN8 · PDBe 6NN8 · UniProt P30613
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