Research workbench
Crystal structure of 3-keto-D-glucoside 4-epimerase, ycjr, from E. COLI, apo form
Analyse Crystal structure of 3-keto-D-glucoside 4-epimerase, ycjr, from E. COLI, apo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WN6
- Type
- protein
- Length
- 1,055 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-keto-D-glucoside 4-epimerase
- UniProt
- A0A5E8GIH3
- Ligands
- MN
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-keto-D-glucoside 4-epimerase | protein | 263 | 44% helix, 16% strand | A0A5E8GIH3 |
| B, C, D | 3-keto-D-glucoside 4-epimerase | protein | 264 | 44% helix, 15% strand | A0A5E8GIH3 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 64 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.63 | 0.74 | 67 | empty |
| 2 | 327 | 0.59 | 0.77 | 28 | EDO |
| 3 | 334 | 0.59 | 0.77 | 31 | EDO |
| 4 | 340 | 0.59 | 0.76 | 31 | EDO |
| 5 | 294 | 0.56 | 0.76 | 27 | EDO |
Interfaces
4 interfaces between chains.
- C–D · 1135 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1112 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6WN6 · Crystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E. coli, apo form · 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 A0A5E8GIH3
- Elsewhere: RCSB PDB 6WN6 · PDBe 6WN6 · UniProt A0A5E8GIH3
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