Research workbench
X-ray analysis of D-xylose isomerase at 1.9 ångströms: native enzyme in complex with substrate and with a mechanism-designed inactivator
Analyse X-ray analysis of D-xylose isomerase at 1.9 ångströms: native enzyme in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9XIA
- Type
- protein
- Length
- 387 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
- DFR, MN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 387 | 50% helix, 10% strand | P24300 |
Ligands and binding sites
- DFR · 3-deoxy-3-methyl-beta-D-fructofuranose · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
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 | 52 | 0.72 | 0.99 | 25 | empty |
| 2 | 469 | 0.65 | 0.77 | 46 | DFR |
| 3 | 99 | 0.50 | 0.82 | 14 | empty |
| 4 | 60 | 0.27 | 0.72 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 9XIA · X-ray analysis of D-xylose isomerase at 1.9 ångströms: native enzyme in complex with… · 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 9XIA · PDBe 9XIA · UniProt P24300
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.