MolNFT v1 · #156611 · protein
Structure of the apo-form of 20BETA-hydroxysteroid dehydrogenase from bifidobacterium adolescentis strain L2-32
6M9U · Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family…: “Structure of the apo-form of 20BETA-hydroxysteroid dehydrogenase from bifidobacterium adolescentis strain…”. X-ray diffraction, 1 ligand (CL), 4 pockets (best…
- PDB
- 6M9U
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein
- UniProt
- A7A7R9
- Ligands
- CL
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein | protein | 251 | 53% helix, 18% strand | A7A7R9 |
| B | Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family protein | protein | 250 | 51% helix, 18% strand | A7A7R9 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.64 | 0.77 | 63 | EDO, PEG |
| 2 | 383 | 0.62 | 0.77 | 41 | EDO, CL |
| 3 | 73 | 0.31 | 0.75 | 17 | empty |
| 4 | 60 | 0.28 | 0.75 | 16 | IPA |
Interfaces
1 interface between chains.
- A–B · 3161 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 6M9U · Structure of the apo-form of 20beta-Hydroxysteroid Dehydrogenase from Bifidobacterium… · 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 A7A7R9
- Elsewhere: RCSB PDB 6M9U · PDBe 6M9U · UniProt A7A7R9
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