MolNFT v1 · #106515 · protein
Crystal structure of pyridoxal kinase from entamoeba histolytica
4S1M: “Crystal structure of pyridoxal kinase from entamoeba histolytica”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.75). MolNFT v1 #106515 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4S1M
- Type
- protein
- Length
- 554 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
- MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase (EC 2.7.1.35) | protein | 279 | 41% helix, 20% strand | C4LVZ4 |
| B | Pyridoxal kinase (EC 2.7.1.35) | protein | 275 | 39% helix, 20% strand | C4LVZ4 |
Ligands and binding sites
- 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
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 | 355 | 0.75 | 0.86 | 54 | MG |
| 2 | 422 | 0.69 | 0.81 | 50 | MG |
| 3 | 94 | 0.61 | 0.88 | 17 | empty |
| 4 | 71 | 0.38 | 0.78 | 18 | empty |
| 5 | 59 | 0.37 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1841 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4S1M · Crystal Structure of Pyridoxal Kinase from Entamoeba histolytica · 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 4S1M · PDBe 4S1M · UniProt C4LVZ4
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