MolNFT v1 · #27934 · protein
The role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino-acid
1XYM: “The role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase…”. X-ray diffraction, 3 ligands (GLO, MG, OH), 11 pockets (best druggability 0.75). MolNFT v1 #27934 on GenesisL1: 3D…
- PDB
- 1XYM
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P15587
- Ligands
- GLO, MG, OH
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xylose isomerase (EC 5.3.1.5) | protein | 386 | 51% helix, 10% strand | P15587 |
Ligands and binding sites
- GLO · D-glucose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.75 | 0.95 | 24 | empty |
| 2 | 134 | 0.73 | 0.93 | 23 | empty |
| 3 | 62 | 0.73 | 0.98 | 22 | empty |
| 4 | 60 | 0.72 | 0.98 | 24 | empty |
| 5 | 429 | 0.72 | 0.83 | 42 | GLO, OH |
Interfaces
1 interface between chains.
- A–B · 1515 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1XYM · The role of the divalent metal ion in sugar binding, ring opening, and isomerization by… · the same entry in another collection · chain A against A, TM-score 1.00
- P15587 · AlphaFold monomer V2.0 prediction for xylose isomerase (P15587) · 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 P15587
- Elsewhere: RCSB PDB 1XYM · PDBe 1XYM · UniProt P15587
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