Research workbench
Structure of human liver pyruvate kinase from which the B domain has been deleted
Analyse Structure of human liver pyruvate kinase from which the B domain has been… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QDN
- Type
- protein
- Length
- 3,415 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
- Ligands
- FBP, OXD, MG, K, NA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 423 | 47% helix, 17% strand | P30613 |
| B | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 436 | 48% helix, 16% strand | P30613 |
| C | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 427 | 46% helix, 17% strand | P30613 |
| D, H | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 425 | 48% helix, 17% strand | P30613 |
| F | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 435 | 49% helix, 16% strand | P30613 |
| G | Pyruvate kinase pklr (EC 2.7.1.40) | protein | 421 | 47% helix, 17% strand | P30613 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 8 copies · chains A, B, C, G, D, E, F, H
- OXD · Oxalic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, 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
- NA · Sodium ion · metal · 6 copies · chains B, C, D, 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 | 1069 | 0.87 | 0.88 | 82 | empty |
| 2 | 329 | 0.86 | 0.96 | 42 | empty |
| 3 | 331 | 0.86 | 0.96 | 41 | empty |
| 4 | 335 | 0.86 | 0.95 | 45 | empty |
| 5 | 336 | 0.86 | 0.95 | 43 | empty |
Interfaces
13 interfaces between chains.
- A–C · 2658 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2652 Ų buried · 38 hydrogen bonds · protein-protein
- E–G · 2647 Ų buried · 39 hydrogen bonds · protein-protein
- F–H · 2629 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1670 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7QDN · Structure of human liver pyruvate kinase from which the B domain has been deleted · 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 7QDN · PDBe 7QDN · UniProt P30613
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.