Research workbench
Pyridoxal kinase of entamoeba histolytica with ADP
Analyse Pyridoxal kinase of entamoeba histolytica with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S1H
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase
- EC
- 2.7.1.35
- UniProt
- C4LVZ4
- Ligands
- ADP, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase (EC 2.7.1.35) | protein | 287 | 38% helix, 20% strand | C4LVZ4 |
| B | Pyridoxal kinase (EC 2.7.1.35) | protein | 279 | 37% helix, 20% strand | C4LVZ4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.79 | 0.87 | 60 | ADP, MG |
| 2 | 438 | 0.76 | 0.85 | 59 | MG, ADP |
| 3 | 97 | 0.62 | 0.88 | 20 | empty |
| 4 | 89 | 0.41 | 0.78 | 16 | empty |
| 5 | 79 | 0.40 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1849 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4S1H · Pyridoxal kinase of Entamoeba histolytica with ADP · 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 C4LVZ4
- Elsewhere: RCSB PDB 4S1H · PDBe 4S1H · UniProt C4LVZ4
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