MolNFT v1 · #184749 · protein
Crystal structure of 3-ketosteroid DELTA1-dehydrogenase from sterolibacterium denitrificans in complex with 1,4-androstadiene-3, 17-dione
7P18 · 3-oxosteroid 1-dehydrogenase: “Crystal structure of 3-ketosteroid DELTA1-dehydrogenase from sterolibacterium denitrificans in complex with…”. X-ray diffraction, 3 ligands (FAD, ANB, NA), 6 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 7P18
- Type
- protein
- Length
- 1,115 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxosteroid 1-dehydrogenase
- EC
- 1.3.99.4
- UniProt
- A9XWD7
- Ligands
- FAD, ANB, NA
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxosteroid 1-dehydrogenase (EC 1.3.99.4) | protein | 558 | 35% helix, 21% strand | A9XWD7 |
| B | 3-oxosteroid 1-dehydrogenase (EC 1.3.99.4) | protein | 557 | 35% helix, 21% strand | A9XWD7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ANB · Androsta-1,4-diene-3,17-dione · ligand · chains A
- NA · Sodium ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.85 | 0.86 | 106 | FAD, ANB, GOL, NA |
| 2 | 1101 | 0.85 | 0.86 | 112 | FAD |
| 3 | 407 | 0.73 | 0.84 | 64 | empty |
| 4 | 84 | 0.31 | 0.73 | 22 | empty |
| 5 | 51 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 552 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7P18 · Crystal structure of 3-ketosteroid delta1-dehydrogenase from Sterolibacterium… · 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 A9XWD7
- Elsewhere: RCSB PDB 7P18 · PDBe 7P18 · UniProt A9XWD7
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