MolNFT v1 · #113890 · protein
The 1.03 ångström structure (P212121) of glucose isomerase crystallized in high-strength agarose hydrogel
5AVN · Xylose isomerase: “The 1.03 ångström structure (P212121) of glucose isomerase crystallized in high-strength agarose hydrogel”. X-ray diffraction, 3 ligands (MN, CA, SO4), 8 pockets (best druggability 0.73). MolNFT v1 #113890 on…
- PDB
- 5AVN
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- MN, CA, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xylose isomerase (EC 5.3.1.5) | protein | 387 | 50% helix, 11% strand | P24300 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.73 | 0.99 | 23 | empty |
| 2 | 55 | 0.72 | 0.99 | 25 | empty |
| 3 | 491 | 0.65 | 0.77 | 54 | SO4 |
| 4 | 445 | 0.62 | 0.76 | 44 | SO4 |
| 5 | 228 | 0.59 | 0.80 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 4791 Ų buried · 80 hydrogen bonds · protein-protein
Compared structures
- 5AVN · The 1.03 angstrom structure (P212121) of glucose isomerase crystallized in high-strength… · 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 5AVN · PDBe 5AVN · UniProt P24300
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