Research workbench
Crystal structure of xylose isomerase domain containing protein (STM4435) from salmonella typhimurium LT2 with unknown ligand
Analyse Crystal structure of xylose isomerase domain containing protein (STM4435) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HGX
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase domain containing protein
- UniProt
- Q8ZK48
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase domain containing protein | protein | 268 | 40% helix, 15% strand | Q8ZK48 |
| B | Xylose isomerase domain containing protein | protein | 271 | 44% helix, 16% strand | Q8ZK48 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.58 | 0.79 | 51 | empty |
| 2 | 78 | 0.54 | 0.85 | 20 | empty |
| 3 | 53 | 0.53 | 0.88 | 21 | empty |
| 4 | 120 | 0.49 | 0.80 | 19 | empty |
| 5 | 102 | 0.43 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4HGX · Crystal structure of xylose isomerase domain containing protein (stm4435) from salmonella… · 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 Q8ZK48
- Elsewhere: RCSB PDB 4HGX · PDBe 4HGX · UniProt Q8ZK48
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