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Crystal structure of plasmodium falciparum hppk-dhps S436F/A437G/A613S with pterin and P-hydrobenzoate
Analyse Crystal structure of plasmodium falciparum hppk-dhps S436F/A437G/A613S with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KCM
- Type
- protein
- Length
- 1,133 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 0.69
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 | 543 | 42% helix, 17% strand | Q25704 |
| B | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase- dihydropteroate synthase | protein | 590 | 43% 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.69 | 0.78 | 66 | PE0, PHB, GOL |
| 2 | 452 | 0.69 | 0.80 | 41 | ATP, MG |
| 3 | 544 | 0.65 | 0.76 | 74 | empty |
| 4 | 264 | 0.58 | 0.78 | 38 | PE0, PHB, GOL |
| 5 | 366 | 0.57 | 0.75 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1973 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6KCM · Crystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/A613S 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 6KCM · PDBe 6KCM · UniProt Q25704
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