Research workbench
Crystal structure of the short chain dehydrogenase from shigella flexneri
Analyse Crystal structure of the short chain dehydrogenase from shigella flexneri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E9Q
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain dehydrogenase
- UniProt
- Q83RM3
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain dehydrogenase | protein | 255 | 45% helix, 14% strand | Q83RM3 |
| B | Short-chain dehydrogenase | protein | 256 | 45% helix, 14% strand | Q83RM3 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.76 | 0.86 | 54 | SO4 |
| 2 | 341 | 0.75 | 0.86 | 53 | SO4 |
| 3 | 66 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1528 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3E9Q · Crystal Structure of the Short Chain Dehydrogenase from Shigella flexneri · 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 Q83RM3
- Elsewhere: RCSB PDB 3E9Q · PDBe 3E9Q · UniProt Q83RM3
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