Research workbench
Crystal structure of plasmodium falciparum pdxk with ligands AMP-pnp and pl
Analyse Crystal structure of plasmodium falciparum pdxk with ligands AMP-pnp and pl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SU9
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase
- EC
- 2.7.1.35
- UniProt
- C6KT01
- Ligands
- ANP, PXL, MG
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase (EC 2.7.1.35) | protein | 295 | 38% helix, 25% strand | C6KT01 |
| B | Pyridoxal kinase (EC 2.7.1.35) | protein | 292 | 39% helix, 27% strand | C6KT01 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- PXL · 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.76 | 0.83 | 55 | ANP, PXL, MG |
| 2 | 536 | 0.74 | 0.82 | 52 | ANP, PXL, MG |
| 3 | 51 | 0.71 | 0.99 | 14 | empty |
| 4 | 214 | 0.49 | 0.75 | 35 | empty |
| 5 | 153 | 0.43 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1619 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6SU9 · Crystal structure of Plasmodium falciparum PdxK with ligands AMP-PNP and PL · 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 C6KT01
- Elsewhere: RCSB PDB 6SU9 · PDBe 6SU9 · UniProt C6KT01
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