MolNFT v1 · #133892 · protein
Structure of liver pyruvate kinase in complex with anthraquinone derivative 15
5SDT: “Structure of liver pyruvate kinase in complex with anthraquinone derivative 15”. X-ray diffraction, 5 ligands (FBP, OXL, I9Q), 20 pockets (best druggability 0.87). MolNFT v1 #133892 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5SDT
- Type
- protein
- Length
- 3,418 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q16716
- Ligands
- FBP, OXL, I9Q, MG, K
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 419 | 48% helix, 17% strand | Q16716 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 436 | 48% helix, 16% strand | Q16716 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 424 | 47% helix, 16% strand | Q16716 |
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 425 | 47% helix, 17% strand | Q16716 |
| E | Pyruvate kinase (EC 2.7.1.40) | protein | 419 | 48% helix, 17% strand | Q16716 |
| F | Pyruvate kinase (EC 2.7.1.40) | protein | 432 | 48% helix, 16% strand | Q16716 |
| G | Pyruvate kinase (EC 2.7.1.40) | protein | 434 | 48% helix, 16% strand | Q16716 |
| H | Pyruvate kinase (EC 2.7.1.40) | protein | 429 | 47% helix, 17% strand | Q16716 |
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
- OXL · Oxalate ion · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- I9Q · N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracene-2-sulfonyl)-beta-alanine · ligand · 6 copies · chains A, B, C, E, F, G
- 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
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 | 360 | 0.87 | 0.96 | 53 | empty |
| 2 | 343 | 0.87 | 0.96 | 41 | empty |
| 3 | 358 | 0.87 | 0.95 | 45 | empty |
| 4 | 333 | 0.86 | 0.95 | 47 | empty |
| 5 | 911 | 0.85 | 0.87 | 66 | empty |
Interfaces
13 interfaces between chains.
- B–D · 2695 Ų buried · 37 hydrogen bonds · protein-protein
- E–G · 2663 Ų buried · 38 hydrogen bonds · protein-protein
- F–H · 2652 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2646 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2000 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5SDT · Structure of liver pyruvate kinase in complex with anthraqui derivative 15 · the same entry in another collection · chain D against D, 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 Q16716
- Elsewhere: RCSB PDB 5SDT · PDBe 5SDT · UniProt Q16716
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