Research workbench
Fructose-1,6-BISPHOSPHATASE(D-fructose-1,6-bisphosphate -1-phosphohydrolase) (E.C.3.1.3.11) complexed with a dual binding AMP site inhibitor
Analyse Fructose-1,6-BISPHOSPHATASE(D-fructose-1,6-bisphosphate -1-phosphohydrolase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VT5
- Type
- protein
- Length
- 2,540 residues
- Chains
- 8
- 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
- ROK
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 319 | 39% helix, 24% strand | P09467 |
| B, C, D, F, G, H | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 317 | 38% helix, 25% strand | P09467 |
Ligands and binding sites
- ROK · 4-amino-N-[(2-sulfanylethyl)carbamoyl]benzenesulfonamide · ligand · 8 copies · chains A, C, B, D, E, G, F, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.84 | 0.84 | 115 | empty |
| 2 | 1084 | 0.83 | 0.84 | 111 | empty |
| 3 | 61 | 0.72 | 0.99 | 28 | empty |
| 4 | 632 | 0.72 | 0.79 | 86 | empty |
| 5 | 59 | 0.71 | 0.98 | 25 | empty |
Interfaces
14 interfaces between chains.
- E–F · 2412 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2412 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2404 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2373 Ų buried · 26 hydrogen bonds · protein-protein
- F–H · 1292 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2VT5 · Fructose-1,6-BISPHOSPHATASE(D-fructose-1,6-bisphosphate -1- phosphohydrolase)… · the same entry in another collection · chain F against F, 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 F 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 2VT5 · PDBe 2VT5 · UniProt P09467
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