MolNFT v1 · #27924 · protein
X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis
1XYC: “X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and…”. X-ray diffraction, 2 ligands (3MF, MG), 10 pockets (best druggability 0.82). MolNFT v1 #27924 on GenesisL1: 3D structure…
- PDB
- 1XYC
- 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
- 3MF, MG
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xylose isomerase (EC 5.3.1.5) | protein | 386 | 50% helix, 10% strand | P15587 |
Ligands and binding sites
- 3MF · 3-O-methylfructose in linear form · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.82 | 0.94 | 43 | empty |
| 2 | 62 | 0.74 | 0.99 | 25 | empty |
| 3 | 54 | 0.72 | 0.99 | 26 | empty |
| 4 | 412 | 0.71 | 0.82 | 42 | 3MF |
| 5 | 419 | 0.70 | 0.81 | 44 | 3MF |
Interfaces
1 interface between chains.
- A–B · 1558 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1XYC · X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the… · 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 1XYC · PDBe 1XYC · UniProt P15587
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