Research workbench
Crystal structure of galaktokinase from pyrococcus horikoshii with AMP-pnp and galactose
Analyse Crystal structure of galaktokinase from pyrococcus horikoshii with AMP-pnp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DEI
- Type
- protein
- Length
- 350 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
- MAP, GLA
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable galactokinase (EC 2.7.1.6) | protein | 350 | 46% helix, 24% strand | O58107 |
Ligands and binding sites
- MAP · Magnesium-5'-adenyly-imido-triphosphate · 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 | 495 | 0.76 | 0.84 | 56 | GLA, MAP |
| 2 | 51 | 0.27 | 0.75 | 13 | empty |
Compared structures
- 2DEI · Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PNP 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 2DEI · PDBe 2DEI · UniProt O58107
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