Research workbench
Structure of dehydrated D-xylose isomerase from streptomyces rubiginosus
Analyse Structure of dehydrated D-xylose isomerase from streptomyces rubiginosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GNX
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- XYL, MN
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Xylose isomerase (EC 5.3.1.5) | protein | 385 | 51% helix, 11% strand | P24300 |
Ligands and binding sites
- XYL · Xylitol · ligand · 2 copies · chains A, E
- MN · Manganese (II) ion · metal · 4 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.78 | 0.80 | 109 | XYL, MN |
| 2 | 52 | 0.71 | 0.99 | 24 | empty |
| 3 | 404 | 0.68 | 0.80 | 46 | XYL, MN |
| 4 | 84 | 0.49 | 0.83 | 13 | empty |
| 5 | 85 | 0.46 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–E · 1544 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3GNX · Structure of dehydrated D-xylose isomerase from streptomyces rubiginosus · 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 3GNX · PDBe 3GNX · UniProt P24300
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