Research workbench
Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift
Analyse Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S5M
- Type
- protein
- Length
- 386 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P15587
- Ligands
- GLC, MN, NA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 386 | 50% helix, 10% strand | P15587 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium 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 | 50 | 0.72 | 0.99 | 20 | empty |
| 2 | 489 | 0.65 | 0.77 | 47 | GLC |
| 3 | 62 | 0.43 | 0.82 | 14 | empty |
| 4 | 73 | 0.30 | 0.73 | 17 | empty |
Compared structures
- 1S5M · Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies… · 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 1S5M · PDBe 1S5M · UniProt P15587
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