Research workbench
New crystal form of glucose isomerase grown in short peptide supramolecular hydrogels
Analyse New crystal form of glucose isomerase grown in short peptide supramolecular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4US6
- Type
- protein
- Length
- 773 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
- MG, CA, NA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 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 | P24300 |
| B | Xylose isomerase (EC 5.3.1.5) | protein | 387 | 50% helix, 11% strand | P24300 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 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 | 63 | 0.74 | 0.99 | 24 | empty |
| 2 | 61 | 0.73 | 0.98 | 24 | empty |
| 3 | 523 | 0.68 | 0.78 | 50 | GOL |
| 4 | 527 | 0.66 | 0.77 | 48 | GOL, NA |
| 5 | 223 | 0.60 | 0.81 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 4797 Ų buried · 82 hydrogen bonds · protein-protein
Compared structures
- 4US6 · New Crystal Form of Glucose Isomerase Grown in Short Peptide Supramolecular Hydrogels · 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 4US6 · PDBe 4US6 · UniProt P24300
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