Research workbench
Crystal structure of an uncharacterized sugar kinase PH1459 from pyrococcus horikoshii in complex with ATP
Analyse Crystal structure of an uncharacterized sugar kinase PH1459 from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GBU
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized sugar kinase PH1459
- EC
- 2.7.1.-
- UniProt
- O59128
- Ligands
- ATP
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Uncharacterized sugar kinase PH1459 (EC 2.7.1.-) | protein | 302 | 39% helix, 25% strand | O59128 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.79 | 0.81 | 72 | empty |
| 2 | 588 | 0.73 | 0.81 | 46 | ATP |
| 3 | 581 | 0.73 | 0.81 | 52 | ATP |
| 4 | 629 | 0.73 | 0.80 | 51 | ATP |
| 5 | 350 | 0.72 | 0.84 | 45 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1287 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1250 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 434 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 375 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 218 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3GBU · Crystal structure of an uncharacterized sugar kinase PH1459 from Pyrococcus horikoshii in… · the same entry in another collection · chain A against A, TM-score 1.00
- O59128 · AlphaFold monomer V2.0 prediction for putative sugar kinase PH1459 (O59128) · 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 O59128
- Elsewhere: RCSB PDB 3GBU · PDBe 3GBU · UniProt O59128
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