MolNFT v1 · #29046 · protein
Crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol- isomerase from enterococcus faecalis
1YWK · 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1: “Crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol- isomerase from enterococcus faecalis”. X-ray diffraction, 17 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 1YWK
- Type
- protein
- Length
- 1,523 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 1
- EC
- 5.3.1.17
- UniProt
- Q838L9
- Pockets
- 17 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1 (EC 5.3.1.17) | protein | 255 | 7% helix, 41% strand | Q838L9 |
| B, E | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1 (EC 5.3.1.17) | protein | 254 | 6% helix, 41% strand | Q838L9 |
| C | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1 (EC 5.3.1.17) | protein | 253 | 7% helix, 41% strand | Q838L9 |
| D | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1 (EC 5.3.1.17) | protein | 254 | 8% helix, 41% strand | Q838L9 |
| F | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1 (EC 5.3.1.17) | protein | 253 | 6% helix, 40% strand | Q838L9 |
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.61 | 0.78 | 44 | empty |
| 2 | 301 | 0.57 | 0.77 | 40 | empty |
| 3 | 362 | 0.54 | 0.74 | 33 | empty |
| 4 | 120 | 0.46 | 0.78 | 26 | empty |
| 5 | 69 | 0.45 | 0.82 | 16 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1180 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1121 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 612 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 539 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1YWK · Crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol-isomerase from… · the same entry in another collection · chain F against F, TM-score 1.00
- Q838L9 · AlphaFold monomer V2.0 prediction for 4-deoxy-L-threo-5-hexosulose- uronate… · a predicted model of the same protein · chain C 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 Q838L9
- Elsewhere: RCSB PDB 1YWK · PDBe 1YWK · UniProt Q838L9
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