MolNFT v1 · #34389 · protein
Crystal structure of galaktokinase from pyrococcus horikoshii with AMP-pn and galactose
2DEJ · Probable galactokinase: “Crystal structure of galaktokinase from pyrococcus horikoshii with AMP-pn and galactose”. X-ray diffraction, 2 ligands (APW, GLA), 2 pockets (best druggability 0.73). MolNFT v1 #34389 on GenesisL1: 3D…
- PDB
- 2DEJ
- Type
- protein
- Length
- 346 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable galactokinase
- EC
- 2.7.1.6
- UniProt
- O58107
- Ligands
- APW, GLA
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable galactokinase (EC 2.7.1.6) | protein | 346 | 45% helix, 25% strand | O58107 |
Ligands and binding sites
- APW · {5'-O-[(R)-{[(S)-amino(hydroxy-kappao)phosphoryl]oxy}(hydroxy-kappao)phosphoryl]adenosinato(2-)}magnesium · ligand · chains A
- GLA · alpha-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.73 | 0.82 | 55 | GLA, APW |
| 2 | 57 | 0.29 | 0.75 | 15 | empty |
Compared structures
- 2DEJ · Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PN and galactose · the same entry in another collection · chain A against A, TM-score 1.00
- O58107 · AlphaFold monomer V2.0 prediction for galactokinase (O58107) · a predicted model of the same protein · 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 O58107
- Elsewhere: RCSB PDB 2DEJ · PDBe 2DEJ · UniProt O58107
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