Research workbench
Crystal structure of plasmodium falciparum hppk-dhps wild type with sdx-dhp
Analyse Crystal structure of plasmodium falciparum hppk-dhps wild type with sdx-dhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JWX
- Type
- protein
- Length
- 1,070 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
- CKL, AMP, PH2, MG, CA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase- dihydropteroate synthase | protein | 544 | 42% helix, 17% strand | Q25704 |
| B | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase- dihydropteroate synthase | protein | 526 | 46% helix, 17% strand | Q25704 |
Ligands and binding sites
- CKL · 4-[(2-azanyl-4-oxidanylidene-7,8-dihydro-3~{H}-pteridin-6-yl)methylamino]-~{N}-(5,6-dimethoxypyrimidin-4-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
- 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 | 447 | 0.68 | 0.79 | 41 | PH2, AMP, MG |
| 2 | 388 | 0.58 | 0.75 | 48 | empty |
| 3 | 225 | 0.57 | 0.79 | 26 | CA |
| 4 | 255 | 0.56 | 0.77 | 33 | CKL, ACT |
| 5 | 193 | 0.54 | 0.79 | 23 | AMP, MG |
Interfaces
1 interface between chains.
- A–B · 1707 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6JWX · Crystal structure of Plasmodium falciparum HPPK-DHPS wild type with SDX-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 6JWX · PDBe 6JWX · UniProt Q25704
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