Research workbench
The crystal structure of ligand bound xylulose kinase from lactobacillus acidophilus
Analyse The crystal structure of ligand bound xylulose kinase from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LL3
- Type
- protein
- Length
- 982 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gluconate kinase
- EC
- 2.7.1.12
- UniProt
- Q5FM28
- Ligands
- DXP, ATP, XUL, ADP
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gluconate kinase (EC 2.7.1.12) | protein | 492 | 40% helix, 23% strand | Q5FM28 |
| B | Gluconate kinase (EC 2.7.1.12) | protein | 490 | 40% helix, 23% strand | Q5FM28 |
Ligands and binding sites
- DXP · 1-deoxy-D-xylulose-5-phosphate · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- XUL · D-xylulose · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.73 | 0.78 | 82 | DXP, XUL |
| 2 | 725 | 0.73 | 0.79 | 72 | DXP |
| 3 | 54 | 0.72 | 0.99 | 23 | empty |
| 4 | 70 | 0.36 | 0.77 | 17 | empty |
| 5 | 71 | 0.32 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1493 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3LL3 · The crystal structure of ligand bound xylulose kinase from Lactobacillus acidophilus · 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 Q5FM28
- Elsewhere: RCSB PDB 3LL3 · PDBe 3LL3 · UniProt Q5FM28
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