Research workbench
Pyridoxal kinase from leishmania donovani in complex with ADP and ginkgotoxin
Analyse Pyridoxal kinase from leishmania donovani in complex with ADP and ginkgotoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K92
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase, putative
- UniProt
- E9BLM4
- Ligands
- ADP, GT0, CA, PO4, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase, putative | protein | 290 | 41% helix, 23% strand | E9BLM4 |
| B | Pyridoxal kinase, putative | protein | 294 | 41% helix, 21% strand | E9BLM4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GT0 · 5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 7 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.79 | 0.87 | 49 | ADP, GT0, CA, PO4 |
| 2 | 440 | 0.78 | 0.86 | 49 | ADP, GT0, CA, PO4 |
| 3 | 95 | 0.78 | 0.99 | 18 | empty |
| 4 | 110 | 0.42 | 0.78 | 23 | empty |
| 5 | 99 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1566 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6K92 · Pyridoxal Kinase from Leishmania donovani in complex with ADP and Ginkgotoxin · 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 E9BLM4
- Elsewhere: RCSB PDB 6K92 · PDBe 6K92 · UniProt E9BLM4
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