Research workbench
Fructose-1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate
Analyse Fructose-1,6-bisphosphate aldolase covalently bound to the substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J4E
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase a
- EC
- 4.1.2.13
- UniProt
- P00883
- Ligands
- 13P
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 341 | 48% helix, 17% strand | P00883 |
Ligands and binding sites
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.85 | 0.86 | 97 | empty |
| 2 | 413 | 0.80 | 0.88 | 54 | empty |
| 3 | 493 | 0.78 | 0.85 | 60 | empty |
| 4 | 149 | 0.63 | 0.86 | 51 | empty |
| 5 | 143 | 0.62 | 0.86 | 50 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1169 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1166 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 924 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 923 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1J4E · Fructose-1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone… · the same entry in another collection · chain D against D, TM-score 1.00
- P00883 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase a (P00883) · a predicted model of the same protein · chain C 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 P00883
- Elsewhere: RCSB PDB 1J4E · PDBe 1J4E · UniProt P00883
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