MolNFT v1 · #154482 · protein
Crystal structure of plasmodium falciparum hppk-dhps A437G/K540E with pterin and P-hydroxybenzoate
6KCL · 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase…: “Crystal structure of plasmodium falciparum hppk-dhps A437G/K540E with pterin and P-hydroxybenzoate”. X-ray diffraction, 5 ligands (PE0, PHB, ATP), 20 pockets (best druggability…
- PDB
- 6KCL
- Type
- protein
- Length
- 1,078 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
- PE0, PHB, ATP, MG, CA
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase- dihydropteroate synthase | protein | 533 | 44% helix, 17% strand | Q25704 |
| B | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase- dihydropteroate synthase | protein | 545 | 46% helix, 16% strand | Q25704 |
Ligands and binding sites
- PE0 · Pterine · ligand · 2 copies · chains A, B
- PHB · P-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.64 | 0.77 | 58 | empty |
| 2 | 335 | 0.61 | 0.78 | 44 | ATP, MG |
| 3 | 204 | 0.58 | 0.80 | 27 | empty |
| 4 | 365 | 0.58 | 0.75 | 46 | empty |
| 5 | 330 | 0.58 | 0.76 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1680 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6KCL · Crystal structure of Plasmodium falciparum HPPK-DHPS A437G/K540E with pterin and… · 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 6KCL · PDBe 6KCL · UniProt Q25704
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