Research workbench
Structure determination of glucose isomerase from streptomyces murinus at 2.6 ångströms resolution
Analyse Structure determination of glucose isomerase from streptomyces murinus at 2.6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DXI
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P37031
- Ligands
- MG
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-xylose isomerase (EC 5.3.1.5) | protein | 388 | 43% helix, 9% strand | P37031 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.98 | 23 | empty |
| 2 | 58 | 0.73 | 0.99 | 20 | empty |
| 3 | 477 | 0.65 | 0.77 | 46 | empty |
| 4 | 281 | 0.64 | 0.81 | 36 | empty |
| 5 | 449 | 0.64 | 0.77 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 4648 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 1DXI · Structure determination of glucose isomerase from streptomyces murinus at 2.6 ångströms… · the same entry in another collection · chain A against A, TM-score 1.00
- P37031 · AlphaFold monomer V2.0 prediction for xylose isomerase (P37031) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P37031
- Elsewhere: RCSB PDB 1DXI · PDBe 1DXI · UniProt P37031
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