MolNFT v1 · #175587 · protein
Human fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate
7CVH: “Human fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate”. X-ray diffraction, 4 ligands (FBP, AMP, GRG), 19 pockets (best druggability 0.85). MolNFT v1 #175587 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7CVH
- Type
- protein
- Length
- 1,278 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphatase 1
- EC
- 3.1.3.11
- UniProt
- P09467
- Ligands
- FBP, AMP, GRG, MG
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 319 | 38% helix, 24% strand | P09467 |
| C | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 318 | 39% helix, 25% strand | P09467 |
| D | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 322 | 38% helix, 25% strand | P09467 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, C, B, D
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, C, B, D
- GRG · Geranylgeranyl diphosphate · ligand · chains A, C, B, D
- MG · Magnesium ion · metal · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.85 | 0.86 | 112 | GRG |
| 2 | 290 | 0.59 | 0.78 | 46 | AMP |
| 3 | 156 | 0.52 | 0.80 | 34 | FBP |
| 4 | 177 | 0.52 | 0.79 | 35 | FBP, MG |
| 5 | 121 | 0.51 | 0.81 | 29 | FBP |
Interfaces
6 interfaces between chains.
- B–D · 2470 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2428 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1285 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1262 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 487 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7CVH · Human Fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate · the same entry in another collection · chain D against D, TM-score 1.00
- P09467 · AlphaFold monomer V2.0 prediction for fructose-1,6-bisphosphatase 1 (P09467) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P09467
- Elsewhere: RCSB PDB 7CVH · PDBe 7CVH · UniProt P09467
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