MolNFT v1 · #27391 · protein
Modes of binding substrates and their analogues to the enzyme D-xylose isomerase
1XIE: “Modes of binding substrates and their analogues to the enzyme D-xylose isomerase”. X-ray diffraction, 2 ligands (ASO, MN), 4 pockets (best druggability 0.73). MolNFT v1 #27391 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1XIE
- Type
- protein
- Length
- 387 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- ASO, MN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-xylose isomerase (EC 5.3.1.5) | protein | 387 | 50% helix, 11% strand | P24300 |
Ligands and binding sites
- ASO · 1,5-anhydro-D-glucitol · 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 | 57 | 0.73 | 0.99 | 23 | empty |
| 2 | 462 | 0.66 | 0.78 | 51 | ASO |
| 3 | 94 | 0.49 | 0.82 | 13 | empty |
| 4 | 68 | 0.28 | 0.72 | 15 | empty |
Compared structures
- 1XIE · Modes of binding substrates and their analogues to the enzyme D-xylose isomerase · the same entry in another collection · chain A against A, TM-score 1.00
- P24300 · AlphaFold monomer V2.0 prediction for xylose isomerase (P24300) · 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 P24300
- Elsewhere: RCSB PDB 1XIE · PDBe 1XIE · UniProt P24300
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