Research workbench
The structure of human liver pyruvate kinase, hlpyk-W527H
Analyse The structure of human liver pyruvate kinase, hlpyk-W527H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NN5
- Type
- protein
- Length
- 1,667 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
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 417 | 49% helix, 16% strand | P30613 |
| B | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 417 | 48% helix, 16% strand | P30613 |
| C | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 413 | 48% helix, 16% strand | P30613 |
| D | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 420 | 48% helix, 16% strand | P30613 |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.86 | 0.87 | 110 | empty |
| 2 | 359 | 0.86 | 0.95 | 43 | EDO |
| 3 | 337 | 0.86 | 0.95 | 47 | EDO |
| 4 | 658 | 0.82 | 0.86 | 71 | empty |
| 5 | 593 | 0.80 | 0.86 | 69 | GOL |
Interfaces
6 interfaces between chains.
- A–D · 2701 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2614 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1693 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1620 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 66 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6NN5 · The structure of human liver pyruvate kinase, hLPYK-W527H · 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 6NN5 · PDBe 6NN5 · UniProt P30613
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