MolNFT v1 · #72546 · protein
X-ray structure of ketohexokinase in complex with AMP-pnp and fructose
3NBV: “X-ray structure of ketohexokinase in complex with AMP-pnp and fructose”. X-ray diffraction, 3 ligands (ANP, FRU, SO4), 5 pockets (best druggability 0.76). MolNFT v1 #72546 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3NBV
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketohexokinase
- EC
- 2.7.1.3
- Ligands
- ANP, FRU, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketohexokinase (EC 2.7.1.3) | protein | 296 | 36% helix, 25% strand | — |
| B | Ketohexokinase (EC 2.7.1.3) | protein | 301 | 35% helix, 25% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.76 | 0.79 | 92 | ANP, SO4 |
| 2 | 637 | 0.75 | 0.81 | 64 | ANP, FRU |
| 3 | 142 | 0.44 | 0.76 | 22 | empty |
| 4 | 107 | 0.43 | 0.78 | 17 | empty |
| 5 | 91 | 0.35 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1659 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3NBV · X-ray Structure of Ketohexokinase in complex with AMP-PNP and fructose · 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
- Elsewhere: RCSB PDB 3NBV · PDBe 3NBV
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