MolNFT v1 · #107954 · protein
New crystal form of glucose isomerase grown in short peptide supramolecular hydrogels
4US6 · Xylose isomerase: “New crystal form of glucose isomerase grown in short peptide supramolecular hydrogels”. X-ray diffraction, 3 ligands (MG, CA, NA), 8 pockets (best druggability 0.74). MolNFT v1 #107954 on GenesisL1: 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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