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Room temperature X-ray structure of D-xylose isomerase in complex with two MG2+ ions and L-ribose
Analyse Room temperature X-ray structure of D-xylose isomerase in complex with two MG2+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QEH
- Type
- protein
- Length
- 388 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- 32O, MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 388 | 51% helix, 10% strand | P24300 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.70 | 0.98 | 23 | empty |
| 2 | 457 | 0.65 | 0.77 | 48 | 32O |
| 3 | 82 | 0.45 | 0.81 | 13 | empty |
| 4 | 60 | 0.35 | 0.78 | 14 | empty |
Compared structures
- 4QEH · Room temperature X-ray structure of D-xylose isomerase in complex with two Mg2+ ions and… · 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 P24300
- Elsewhere: RCSB PDB 4QEH · PDBe 4QEH · UniProt P24300
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