Research workbench
6-phosphofructo-2-KINASE/FRUCTOSE-2,6-bisphosphatase H256A mutant with F6P in phosphatase active site
Analyse 6-phosphofructo-2-KINASE/FRUCTOSE-2,6-bisphosphatase H256A mutant with F6P in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BIF
- Type
- protein
- Length
- 864 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (6-phosphofructo-2-KINASE/FRUCTOSE-2,6- bisphosphatase)
- EC
- 2.7.1.105, 3.1.3.46
- UniProt
- P25114
- Ligands
- F6P, ANP, MG, PO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (6-phosphofructo-2-KINASE/FRUCTOSE-2,6- bisphosphatase) (EC 2.7.1.105, 3.1.3.46) | protein | 432 | 44% helix, 15% strand | P25114 |
Ligands and binding sites
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.82 | 0.83 | 102 | PO4, SIN |
| 2 | 855 | 0.82 | 0.84 | 82 | BOG, MG, ANP, SIN |
| 3 | 163 | 0.78 | 0.95 | 36 | F6P, PO4 |
| 4 | 173 | 0.78 | 0.94 | 41 | F6P, PO4 |
| 5 | 803 | 0.77 | 0.81 | 86 | BOG |
Interfaces
1 interface between chains.
- A–B · 1049 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2BIF · 6-phosphofructo-2-KINASE/FRUCTOSE-2,6-bisphosphatase H256A mutant with F6P in phosphatase… · the same entry in another collection · chain A against A, TM-score 1.00
- P25114 · AlphaFold monomer V2.0 prediction for 6-phosphofructo-2-KINASE/FRUCTOSE-2,6-bisphosphatase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P25114
- Elsewhere: RCSB PDB 2BIF · PDBe 2BIF · UniProt P25114
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