Research workbench
Pyridoxal kinase of entamoeba histolytica with plp
Analyse Pyridoxal kinase of entamoeba histolytica with plp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S1I
- Type
- protein
- Length
- 555 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
- PLP, MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase (EC 2.7.1.35) | protein | 280 | 39% helix, 20% strand | C4LVZ4 |
| B | Pyridoxal kinase (EC 2.7.1.35) | protein | 275 | 40% helix, 17% strand | C4LVZ4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.74 | 0.84 | 49 | MG, PLP |
| 2 | 344 | 0.73 | 0.85 | 45 | PLP, MG |
| 3 | 91 | 0.62 | 0.89 | 19 | empty |
| 4 | 133 | 0.51 | 0.80 | 29 | empty |
| 5 | 133 | 0.48 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1734 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 4S1I · Pyridoxal Kinase of Entamoeba histolytica with PLP · the same entry in another collection · chain B against B, 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 4S1I · PDBe 4S1I · UniProt C4LVZ4
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