Research workbench
Dipeptide gly-pro binds to a glycolytic enzyme fructose bisphosphate aldolase
Analyse Dipeptide gly-pro binds to a glycolytic enzyme fructose bisphosphate aldolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RNG
- Type
- protein
- Length
- 1,348 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase 6, cytosolic
- EC
- 4.1.2.13
- UniProt
- Q9SJQ9
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Fructose-bisphosphate aldolase 6, cytosolic (EC 4.1.2.13) | protein | 337 | 45% helix, 17% strand | Q9SJQ9 |
| B | Fructose-bisphosphate aldolase 6, cytosolic (EC 4.1.2.13) | protein | 336 | 46% helix, 17% strand | Q9SJQ9 |
| G | Fructose-bisphosphate aldolase 6, cytosolic (EC 4.1.2.13) | protein | 338 | 47% helix, 17% strand | Q9SJQ9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.64 | 0.80 | 53 | empty |
| 2 | 491 | 0.62 | 0.75 | 47 | empty |
| 3 | 212 | 0.57 | 0.80 | 42 | SO4 |
| 4 | 205 | 0.57 | 0.80 | 40 | SO4 |
| 5 | 67 | 0.48 | 0.84 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–F · 327 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 178 Ų buried · 0 hydrogen bonds · protein-protein
- F–G · 167 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6RNG · Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase · the same entry in another collection · chain G against G, TM-score 1.00
- Q9SJQ9 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase 6, cytosolic (Q9SJQ9) · a predicted model of the same protein · chain A 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 Q9SJQ9
- Elsewhere: RCSB PDB 6RNG · PDBe 6RNG · UniProt Q9SJQ9
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