MolNFT v1 · #27502 · protein
D254E, D256E mutant of D-xylose isomerase complexed with AL3 and xylitol
1XLM: “D254E, D256E mutant of D-xylose isomerase complexed with AL3 and xylitol”. X-ray diffraction, 2 ligands (XYL, AL), 8 pockets (best druggability 0.78). MolNFT v1 #27502 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XLM
- 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, AL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-xylose isomerase (EC 5.3.1.5) | protein | 393 | 49% helix, 10% strand | P12070 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.78 | 0.99 | 24 | empty |
| 2 | 88 | 0.77 | 0.98 | 24 | empty |
| 3 | 1139 | 0.76 | 0.78 | 97 | XYL |
| 4 | 913 | 0.72 | 0.77 | 82 | XYL |
| 5 | 111 | 0.42 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1637 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1XLM · D254E, D256E mutant of D-xylose isomerase complexed with AL3 and xylitol · 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 1XLM · PDBe 1XLM · UniProt P12070
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