Research workbench
D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7-bisphosphatase of synechocystis sp. pcc 6803
Analyse D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7-bisphosphatase of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ROJ
- Type
- protein
- Length
- 1,385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7- bisphosphatase
- EC
- 3.1.3.11, 3.1.3.37
- UniProt
- P73922
- Ligands
- AMP, MG, CL, SO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7- bisphosphatase (EC 3.1.3.11, 3.1.3.37) | protein | 347 | 33% helix, 27% strand | P73922 |
| B | D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7- bisphosphatase (EC 3.1.3.11, 3.1.3.37) | protein | 345 | 33% helix, 27% strand | P73922 |
| D | D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7- bisphosphatase (EC 3.1.3.11, 3.1.3.37) | protein | 346 | 32% helix, 27% strand | P73922 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 23 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.85 | 0.88 | 126 | CL, AMP |
| 2 | 423 | 0.81 | 0.89 | 65 | CL |
| 3 | 203 | 0.70 | 0.87 | 37 | AMP |
| 4 | 182 | 0.68 | 0.87 | 29 | AMP |
| 5 | 168 | 0.67 | 0.87 | 28 | AMP |
Interfaces
6 interfaces between chains.
- A–D · 1753 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1715 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1424 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1378 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, oxidation).
Compared structures
- 3ROJ · D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis… · the same entry in another collection · chain D against D, TM-score 1.00
- P73922 · AlphaFold monomer V2.0 prediction for D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE… · a predicted model of the same protein · chain B 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
- Every structure of UniProt P73922
- Elsewhere: RCSB PDB 3ROJ · PDBe 3ROJ · UniProt P73922
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