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A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 ångströms streptomyces rubiginosus structures with xylitol and D-xylose
Analyse A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3XIS
- Type
- protein
- Length
- 385 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Streptomyces rubiginosus
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- XYS, XLS, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 385 | 51% helix, 11% strand | P24300 |
Ligands and binding sites
- XYS · alpha-D-xylopyranose · sugar · chains A
- XLS · D-xylose · sugar · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.73 | 0.98 | 24 | empty |
| 2 | 475 | 0.64 | 0.77 | 51 | XYS, XLS, MG |
| 3 | 98 | 0.50 | 0.82 | 14 | empty |
Compared structures
- 3XIS · A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 ångströms… · the same entry in another collection · chain A against A, TM-score 1.00
- P24300 · AlphaFold monomer V2.0 prediction for xylose isomerase (P24300) · 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 P24300
- Elsewhere: RCSB PDB 3XIS · PDBe 3XIS · UniProt P24300
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