MolNFT v1 · #61238 · protein
Dihydroxyacetone phosphate schiff base and enamine intermediates in D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle
3DFO · Fructose-bisphosphate aldolase a: “Dihydroxyacetone phosphate schiff base and enamine intermediates in D33N mutant fructose-1,6-bisphosphate…”. X-ray diffraction, 1 ligand (13P), 18 pockets (best druggability 0.88). MolNFT v1 #61238…
- PDB
- 3DFO
- Type
- protein
- Length
- 1,411 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 | 46% helix, 15% strand | P00883 |
| C | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 351 | 46% helix, 15% strand | P00883 |
| D | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 360 | 45% helix, 15% 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 | 1027 | 0.88 | 0.90 | 118 | empty |
| 2 | 531 | 0.84 | 0.90 | 72 | empty |
| 3 | 634 | 0.80 | 0.85 | 83 | empty |
| 4 | 319 | 0.66 | 0.82 | 34 | 13P |
| 5 | 155 | 0.65 | 0.87 | 49 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1680 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1539 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1221 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1214 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 103 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3DFO · Dihydroxyacetone phosphate Schiff base and enamine intermediates in D33N 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 3DFO · PDBe 3DFO · UniProt P00883
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