Research workbench
Crystal structure of 5-keto-4-deoxyuronate isomerase from eschericia COLI
Analyse Crystal structure of 5-keto-4-deoxyuronate isomerase from eschericia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XRU
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
- EC
- 5.3.1.17
- UniProt
- Q46938
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (EC 5.3.1.17) | protein | 281 | 10% helix, 43% strand | Q46938 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.97 | 14 | empty |
| 2 | 245 | 0.59 | 0.79 | 29 | 1PE |
| 3 | 219 | 0.58 | 0.79 | 24 | 1PE |
Interfaces
1 interface between chains.
- A–B · 1533 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 1XRU · Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli · the same entry in another collection · chain A against A, TM-score 1.00
- Q46938 · AlphaFold monomer V2.0 prediction for 4-deoxy-L-threo-5-hexosulose- uronate… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q46938
- Elsewhere: RCSB PDB 1XRU · PDBe 1XRU · UniProt Q46938
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