MolNFT v1 · #139520 · protein
Structures of D-xylose isomerase from arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 ångströms and 2.3 ångströms resolution, respectively
5XIA: “Structures of D-xylose isomerase from arthrobacter strain B3728 containing the inhibitors xylitol and…”. X-ray diffraction, 2 ligands (XYL, MG), 9 pockets (best druggability 0.76). MolNFT v1 #139520 on GenesisL1: 3D structure…
- PDB
- 5XIA
- 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
- XYL, MG
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-xylose isomerase (EC 5.3.1.5) | protein | 393 | 47% helix, 10% strand | P12070 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.76 | 0.98 | 28 | empty |
| 2 | 60 | 0.74 | 0.99 | 24 | empty |
| 3 | 647 | 0.73 | 0.79 | 70 | XYL |
| 4 | 240 | 0.71 | 0.87 | 29 | empty |
| 5 | 363 | 0.63 | 0.78 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1679 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5XIA · Structures of D-xylose isomerase from arthrobacter strain B3728 containing the inhibitors… · 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 5XIA · PDBe 5XIA · UniProt P12070
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