Research workbench
Crystal structure of human galactokinase complexed with mgamppnp and galactose
Analyse Crystal structure of human galactokinase complexed with mgamppnp and galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WUU
- Type
- protein
- Length
- 1,561 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- EC
- 2.7.1.6
- UniProt
- P51570
- Ligands
- ANP, GLA, MG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase (EC 2.7.1.6) | protein | 391 | 41% helix, 24% strand | P51570 |
| B | Galactokinase (EC 2.7.1.6) | protein | 390 | 40% helix, 25% strand | P51570 |
| C | Galactokinase (EC 2.7.1.6) | protein | 390 | 41% helix, 23% strand | P51570 |
| D | Galactokinase (EC 2.7.1.6) | protein | 390 | 41% helix, 25% strand | P51570 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.79 | 0.87 | 58 | GLA, MG, ANP |
| 2 | 1177 | 0.78 | 0.80 | 97 | empty |
| 3 | 441 | 0.77 | 0.86 | 51 | GLA, MG, ANP |
| 4 | 480 | 0.76 | 0.85 | 54 | GLA, MG, ANP |
| 5 | 508 | 0.76 | 0.84 | 62 | GLA, MG, ANP |
Interfaces
3 interfaces between chains.
- C–D · 887 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 745 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 354 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 1WUU · crystal structure of human galactokinase complexed with MgAMPPNP and galactose · the same entry in another collection · chain D against D, TM-score 1.00
- P51570 · AlphaFold monomer V2.0 prediction for galactokinase (P51570) · a predicted model of the same protein · chain C 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 P51570
- Elsewhere: RCSB PDB 1WUU · PDBe 1WUU · UniProt P51570
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