MolNFT v1 · #16316 · protein
Fructose-1,6-bisphosphatase complex with AMP, magnesium, fructose-6- phosphate, phosphate and thallium (20 mm)
1NV7: “Fructose-1,6-bisphosphatase complex with AMP, magnesium, fructose-6- phosphate, phosphate and thallium (20 mm)”. X-ray diffraction, 5 ligands (F6P, AMP, TL), 8 pockets (best druggability 0.56). MolNFT v1 #16316 on GenesisL1: 3D…
- PDB
- 1NV7
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphatase
- EC
- 3.1.3.11
- UniProt
- P00636
- Ligands
- F6P, AMP, TL, MG, PO4
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructose-1,6-bisphosphatase (EC 3.1.3.11) | protein | 327 | 37% helix, 24% strand | P00636 |
Ligands and binding sites
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- TL · Thallium (I) ion · metal · 8 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.56 | 0.75 | 42 | empty |
| 2 | 179 | 0.55 | 0.80 | 36 | F6P, PO4, TL |
| 3 | 161 | 0.53 | 0.80 | 31 | F6P, PO4, TL |
| 4 | 139 | 0.51 | 0.80 | 23 | empty |
| 5 | 150 | 0.46 | 0.77 | 26 | AMP |
Interfaces
1 interface between chains.
- A–B · 2424 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 1NV7 · Fructose-1,6-Bisphosphatase Complex With AMP, Magnesium, Fructose-6-Phosphate, Phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- P00636 · AlphaFold monomer V2.0 prediction for fructose-1,6-bisphosphatase 1 (P00636) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P00636
- Elsewhere: RCSB PDB 1NV7 · PDBe 1NV7 · UniProt P00636
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