MolNFT v1 · #93910 · protein
Crystal structure of xylose isomerase domain containing protein (STM4435) from salmonella typhimurium LT2 with unknown ligand
4HGX: “Crystal structure of xylose isomerase domain containing protein (STM4435) from salmonella typhimurium LT2…”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.58). MolNFT v1 #93910 on GenesisL1: 3D structure, binding…
- 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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