Research workbench
Crystal structure of native xylose isomerase from piromyces E2 grown in yeast, in complex with xylose
Analyse Crystal structure of native xylose isomerase from piromyces E2 grown in yeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T8E
- Type
- protein
- Length
- 1,744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- Q9P8C9
- Ligands
- XLS, XYS, XYP, CA, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xylose isomerase (EC 5.3.1.5) | protein | 436 | 49% helix, 12% strand | Q9P8C9 |
Ligands and binding sites
- XLS · D-xylose · ligand · 4 copies · chains A, B, C, D
- XYS · alpha-D-xylopyranose · sugar · 11 copies · chains A, D, C, B
- XYP · beta-D-xylopyranose · sugar · 7 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.86 | 0.94 | 61 | empty |
| 2 | 925 | 0.86 | 0.87 | 85 | empty |
| 3 | 1055 | 0.85 | 0.86 | 119 | XLS |
| 4 | 1069 | 0.84 | 0.85 | 118 | XLS |
| 5 | 190 | 0.79 | 0.94 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4319 Ų buried · 54 hydrogen bonds · protein-protein
- A–D · 4318 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 1990 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1988 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1507 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6T8E · Crystal structure of native xylose isomerase from Piromyces E2 grown in yeast, in complex… · 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 Q9P8C9
- Elsewhere: RCSB PDB 6T8E · PDBe 6T8E · UniProt Q9P8C9
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