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Fructose-1,6-bisphosphate schiff base intermediate in fbp aldolase from leishmania mexicana
Analyse Fructose-1,6-bisphosphate schiff base intermediate in fbp aldolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QDG
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphate aldolase
- EC
- 4.1.2.13
- UniProt
- Q9U5N6
- Ligands
- 2FP, PO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) | protein | 366 | 45% helix, 16% strand | Q9U5N6 |
| C, D | Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) | protein | 358 | 48% helix, 17% strand | Q9U5N6 |
Ligands and binding sites
- 2FP · 1,6-fructose diphosphate (linear form) · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.85 | 0.86 | 104 | empty |
| 2 | 150 | 0.75 | 0.92 | 32 | empty |
| 3 | 179 | 0.73 | 0.90 | 37 | empty |
| 4 | 365 | 0.67 | 0.81 | 40 | PO4, 2FP |
| 5 | 399 | 0.66 | 0.79 | 45 | PO4, 2FP |
Interfaces
6 interfaces between chains.
- B–C · 1556 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1546 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1520 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1507 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 577 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2QDG · Fructose-1,6-bisphosphate Schiff base intermediate in FBP aldolase from Leishmania… · the same entry in another collection · 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 Q9U5N6
- Elsewhere: RCSB PDB 2QDG · PDBe 2QDG · UniProt Q9U5N6
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