Research workbench
Crystal structure of 3-ketosteroid DELTA1-dehydrogenase from rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
Analyse Crystal structure of 3-ketosteroid DELTA1-dehydrogenase from rhodococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C3Y
- Type
- protein
- Length
- 4,052 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-ketosteroid dehydrogenase
- EC
- 1.3.99.4
- UniProt
- Q9RA02
- Ligands
- FAD, ANB, NA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, H | 3-ketosteroid dehydrogenase (EC 1.3.99.4) | protein | 508 | 33% helix, 23% strand | Q9RA02 |
| B, C, F, G | 3-ketosteroid dehydrogenase (EC 1.3.99.4) | protein | 505 | 33% helix, 24% strand | Q9RA02 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ANB · Androsta-1,4-diene-3,17-dione · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
- PG4 · Tetraethylene glycol · additive · 6 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.90 | 0.92 | 192 | FAD, PG4, ANB |
| 2 | 622 | 0.86 | 0.91 | 88 | FAD, ANB |
| 3 | 497 | 0.84 | 0.91 | 69 | FAD, ANB |
| 4 | 477 | 0.84 | 0.91 | 71 | FAD, ANB |
| 5 | 458 | 0.84 | 0.91 | 69 | FAD, ANB |
Interfaces
12 interfaces between chains.
- C–D · 845 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 828 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 826 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 813 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 640 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4C3Y · Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1… · the same entry in another collection · chain F against F, 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 Q9RA02
- Elsewhere: RCSB PDB 4C3Y · PDBe 4C3Y · UniProt Q9RA02
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.