MolNFT v1 · #158211 · protein
The structure of human liver pyruvate kinase, hlpyk-ggg
6NN7 · Pyruvate kinase pklr: “The structure of human liver pyruvate kinase, hlpyk-ggg”. X-ray diffraction, 20 pockets (best druggability 0.87). MolNFT v1 #158211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NN7
- Type
- protein
- Length
- 3,741 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 0.87
Structure
x-ray diffraction · 8 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 516 | 41% helix, 21% strand | P30613 |
| B | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 414 | 49% helix, 16% strand | P30613 |
| C | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 514 | 40% helix, 21% strand | P30613 |
| E | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 518 | 39% helix, 22% strand | P30613 |
| D | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 479 | 41% helix, 18% strand | P30613 |
| F | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 406 | 47% helix, 16% strand | P30613 |
| G | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 496 | 43% helix, 20% strand | P30613 |
| H | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 398 | 48% helix, 17% strand | P30613 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, E, G, D, F
- GOL · Glycerol · additive · 14 copies · chains A, B, C, E, D, F, G, H
- FLC · Citrate anion · additive · 2 copies · chains C, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.87 | 0.95 | 56 | EDO |
| 2 | 365 | 0.87 | 0.95 | 44 | empty |
| 3 | 391 | 0.87 | 0.95 | 49 | empty |
| 4 | 379 | 0.86 | 0.95 | 42 | empty |
| 5 | 1110 | 0.86 | 0.87 | 96 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2804 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 2752 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2748 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2669 Ų buried · 42 hydrogen bonds · protein-protein
- E–G · 1811 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6NN7 · The structure of human liver pyruvate kinase, hLPYK-GGG · 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 6NN7 · PDBe 6NN7 · UniProt P30613
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