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Ternary co-crystal structure of fructose-bisphosphate aldolase from plasmodium falciparum in complex with trap and a small molecule inhibitor
Analyse Ternary co-crystal structure of fructose-bisphosphate aldolase from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TR9
- Type
- protein
- Length
- 1,421 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase; Ala-ala-ser-leu-tyr-glu-lys-lys-ala-ala…
- EC
- 4.1.2.13
- UniProt
- Q7KQL9
- Ligands
- 38D
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 347 | 49% helix, 16% strand | Q7KQL9 |
| E | Ala-ala-ser-leu-tyr-glu-lys-lys-ala-ala | protein | 10 | 60% helix, 0% strand | — |
| G | Ala-ala-ala-ser-leu-tyr-glu-lys-lys-ala-ala | protein | 11 | 36% helix, 0% strand | — |
| H, I, J, K | Asp-TRP-asn | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 38D · N'-[(E)-(2,4-dichlorophenyl)methylidene]-3,4-dihydroxybenzohydrazide · ligand · 4 copies · chains A, H, B, I, C, J, D, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.89 | 0.90 | 125 | empty |
| 2 | 71 | 0.74 | 0.98 | 17 | empty |
| 3 | 78 | 0.74 | 0.98 | 24 | empty |
| 4 | 69 | 0.74 | 0.98 | 16 | empty |
| 5 | 92 | 0.68 | 0.92 | 32 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1535 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1502 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1380 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1356 Ų buried · 18 hydrogen bonds · protein-protein
- B–I · 412 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4TR9 · Ternary co-crystal structure of fructose-bisphosphate aldolase from Plasmodium falciparum… · the same entry in another collection · chain K against K, TM-score 1.00
- Q7KQL9 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase (Q7KQL9) · 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 Q7KQL9
- Elsewhere: RCSB PDB 4TR9 · PDBe 4TR9 · UniProt Q7KQL9
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