Research workbench
Crystal structure of trypanosoma cruzi glucokinase in complex with inhibitor benz-glcn
Analyse Crystal structure of trypanosoma cruzi glucokinase in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BRD
- Type
- protein
- Length
- 734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase 1, putative
- EC
- 2.7.1.2
- UniProt
- Q4E4E1
- Ligands
- BG8
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucokinase 1, putative (EC 2.7.1.2) | protein | 367 | 41% helix, 24% strand | Q4E4E1 |
Ligands and binding sites
- BG8 · 2-(benzoylamino)-2-deoxy-beta-D-glucopyranose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.71 | 0.80 | 58 | BG8 |
| 2 | 581 | 0.71 | 0.80 | 59 | BG8 |
| 3 | 173 | 0.68 | 0.87 | 29 | empty |
| 4 | 167 | 0.63 | 0.84 | 30 | empty |
| 5 | 126 | 0.52 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1954 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5BRD · Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor BENZ-GlcN · the same entry in another collection · 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 Q4E4E1
- Elsewhere: RCSB PDB 5BRD · PDBe 5BRD · UniProt Q4E4E1
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