Research workbench
Dihydroxyacetone phosphate schiff base intermediate in D33S mutant fructose-1,6-bisphosphate aldolase from rabbit muscle
Analyse Dihydroxyacetone phosphate schiff base intermediate in D33S mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DFS
- Type
- protein
- Length
- 1,413 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
- 18 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 350 | 47% helix, 15% strand | P00883 |
| C | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 353 | 46% helix, 15% strand | P00883 |
| D | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 360 | 44% helix, 14% 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
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 | 1014 | 0.88 | 0.90 | 117 | empty |
| 2 | 567 | 0.84 | 0.89 | 75 | empty |
| 3 | 627 | 0.81 | 0.86 | 84 | empty |
| 4 | 348 | 0.67 | 0.81 | 37 | 13P |
| 5 | 166 | 0.66 | 0.87 | 46 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1664 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1530 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1222 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1207 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 95 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3DFS · Dihydroxyacetone phosphate Schiff base intermediate in D33S mutant… · 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 D 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 3DFS · PDBe 3DFS · UniProt P00883
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