MolNFT v1 · #191535 · protein
X-ray analysis of D-xylose isomerase at 1.9 ångströms: native enzyme in complex with substrate and with a mechanism-designed inactivator
8XIA: “X-ray analysis of D-xylose isomerase at 1.9 ångströms: native enzyme in complex with substrate and with a…”. X-ray diffraction, 2 ligands (XLS, MN), 4 pockets (best druggability 0.73). MolNFT v1 #191535 on GenesisL1: 3D structure…
- PDB
- 8XIA
- Type
- protein
- Length
- 387 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- XLS, MN
- Pockets
- 4 · best druggability 0.73
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 | 387 | 50% helix, 10% strand | P24300 |
Ligands and binding sites
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 | 56 | 0.73 | 0.99 | 23 | empty |
| 2 | 457 | 0.65 | 0.78 | 47 | XLS |
| 3 | 101 | 0.49 | 0.81 | 14 | empty |
| 4 | 65 | 0.38 | 0.79 | 13 | empty |
Compared structures
- 8XIA · X-ray analysis of D-xylose isomerase at 1.9 ångströms: native enzyme in complex with… · the same entry in another collection · 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 P24300
- Elsewhere: RCSB PDB 8XIA · PDBe 8XIA · UniProt P24300
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