Research workbench
Crystal structure of mutant xylose isomerase (V270A/A273G) from piromyces E2 grown in yeast, in complex with xylose
Analyse Crystal structure of mutant xylose isomerase (V270A/A273G) from piromyces E2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T8F
- 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 0.89
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 · 8 copies · chains A, C, B, D
- XYP · beta-D-xylopyranose · sugar · 6 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.89 | 0.91 | 123 | empty |
| 2 | 1135 | 0.87 | 0.89 | 144 | XLS |
| 3 | 1095 | 0.85 | 0.86 | 116 | XLS |
| 4 | 212 | 0.79 | 0.93 | 37 | empty |
| 5 | 341 | 0.73 | 0.85 | 57 | empty |
Interfaces
6 interfaces between chains.
- A–D · 4331 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 4316 Ų buried · 57 hydrogen bonds · protein-protein
- B–D · 1987 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1987 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1497 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6T8F · Crystal structure of mutant xylose isomerase (V270A/A273G) from Piromyces E2 grown in… · 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 6T8F · PDBe 6T8F · UniProt Q9P8C9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.