MolNFT v1 · #27500 · protein
Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening followed by a 1,2-hydride shift
1XLK: “Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening followed by a…”. X-ray diffraction, 1 ligand (MN), 11 pockets (best druggability 0.76). MolNFT v1 #27500 on GenesisL1: 3D structure, binding…
- PDB
- 1XLK
- 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
- MN
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-xylose isomerase (EC 5.3.1.5) | protein | 393 | 48% helix, 10% strand | P12070 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.76 | 0.99 | 25 | empty |
| 2 | 75 | 0.75 | 0.98 | 24 | empty |
| 3 | 635 | 0.72 | 0.79 | 66 | empty |
| 4 | 233 | 0.71 | 0.87 | 27 | empty |
| 5 | 349 | 0.62 | 0.78 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1XLK · Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening… · 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 1XLK · PDBe 1XLK · UniProt P12070
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