MolNFT v1 · #31086 · protein
Crystal structure of saccharomyces cerevisiae galactokinase in complex with galactose and MG:AMPPNP
2AJ4: “Crystal structure of saccharomyces cerevisiae galactokinase in complex with galactose and MG:AMPPNP”. X-ray diffraction, 4 ligands (ANP, GLA, MG), 6 pockets (best druggability 0.75). MolNFT v1 #31086 on GenesisL1: 3D structure…
- PDB
- 2AJ4
- Type
- protein
- Length
- 1,014 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- EC
- 2.7.1.6
- UniProt
- P04385
- Ligands
- ANP, GLA, MG, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase (EC 2.7.1.6) | protein | 509 | 46% helix, 18% strand | P04385 |
| B | Galactokinase (EC 2.7.1.6) | protein | 505 | 46% helix, 18% strand | P04385 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 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 | 320 | 0.75 | 0.87 | 53 | GLA, MG, ANP |
| 2 | 395 | 0.74 | 0.84 | 67 | GLA, MG, ANP |
| 3 | 310 | 0.58 | 0.77 | 32 | empty |
| 4 | 279 | 0.55 | 0.76 | 31 | empty |
| 5 | 97 | 0.41 | 0.77 | 19 | empty |
Compared structures
- 2AJ4 · Crystal structure of Saccharomyces cerevisiae Galactokinase in complex with galactose and… · the same entry in another collection · chain A against A, TM-score 1.00
- P04385 · AlphaFold monomer V2.0 prediction for galactokinase (P04385) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P04385
- Elsewhere: RCSB PDB 2AJ4 · PDBe 2AJ4 · UniProt P04385
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