MolNFT v1 · #27067 · protein
X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from escherichia COLI
1X8M · 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase: “X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from escherichia COLI”. X-ray diffraction, 17 pockets (best druggability 0.76). MolNFT v1 #27067 on…
- PDB
- 1X8M
- Type
- protein
- Length
- 1,554 residues
- Chains
- 6
- 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
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (EC 5.3.1.17) | protein | 259 | 9% helix, 41% strand | Q46938 |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.76 | 0.79 | 101 | empty |
| 2 | 86 | 0.72 | 0.96 | 24 | empty |
| 3 | 493 | 0.71 | 0.81 | 58 | empty |
| 4 | 343 | 0.70 | 0.83 | 40 | empty |
| 5 | 715 | 0.68 | 0.76 | 60 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1307 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 937 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 378 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 291 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 240 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1X8M · X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from… · the same entry in another collection · chain C against C, 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 1X8M · PDBe 1X8M · UniProt Q46938
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