Research workbench
Crystal structure of plasmodium falciparum hppk-dhps wild type with stz-dhp
Analyse Crystal structure of plasmodium falciparum hppk-dhps wild type with stz-dhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JWU
- Type
- protein
- Length
- 1,092 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase- dihydropteroate synthase
- UniProt
- Q25704
- Ligands
- XTZ, AMP, PH2, MG, CA, PO4
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase- dihydropteroate synthase | protein | 558 | 42% helix, 16% strand | Q25704 |
| B | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase- dihydropteroate synthase | protein | 534 | 45% helix, 17% strand | Q25704 |
Ligands and binding sites
- XTZ · 4-{[(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl) methyl]amino}-N-(1,3-thiazol-2-yl)benzenesulfonamide · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- PH2 · 2-amino-6-hydroxymethyl-7,8-dihydro-3H-pteridin-4-one · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A
- ACT · Acetate ion · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.65 | 0.79 | 40 | PH2, AMP, MG |
| 2 | 356 | 0.64 | 0.79 | 41 | XTZ, PO4 |
| 3 | 429 | 0.60 | 0.75 | 48 | empty |
| 4 | 365 | 0.59 | 0.76 | 47 | ACT, PO4 |
| 5 | 275 | 0.57 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1701 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6JWU · Crystal structure of Plasmodium falciparum HPPK-DHPS wild type with STZ-DHP · 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 Q25704
- Elsewhere: RCSB PDB 6JWU · PDBe 6JWU · UniProt Q25704
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