Research workbench
Observations of reaction intermediates and the mechanism of aldose- ketose interconversion by D-xylose isomerase
Analyse Observations of reaction intermediates and the mechanism of aldose- ketose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DID
- Type
- protein
- Length
- 786 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
- P12070
- Ligands
- DIG, MN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-xylose isomerase (EC 5.3.1.5) | protein | 393 | 48% helix, 10% strand | P12070 |
Ligands and binding sites
- DIG · 2,5-dideoxy-2,5-imino-D-glucitol · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.76 | 0.78 | 103 | DIG |
| 2 | 73 | 0.76 | 0.99 | 26 | empty |
| 3 | 58 | 0.73 | 0.98 | 22 | empty |
| 4 | 855 | 0.72 | 0.77 | 77 | DIG |
| 5 | 116 | 0.44 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1DID · Observations of reaction intermediates and the mechanism of aldose-ketose interconversion… · the same entry in another collection · chain A against A, TM-score 1.00
- P12070 · AlphaFold monomer V2.0 prediction for xylose isomerase (P12070) · 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 P12070
- Elsewhere: RCSB PDB 1DID · PDBe 1DID · UniProt P12070
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