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Crystal structure of 3-ketosteroid DELTA1-dehydrogenase from rhodococcus erythropolis SQ1
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
- 4C3X
- 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, GLC, FRU, NA, CL
- Pockets
- 20 · best druggability 0.88
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, 23% strand | Q9RA02 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F, G, H
- FRU · beta-D-fructofuranose · sugar · 12 copies · chains A, B, D, C, F, E, H, G
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- PG4 · Tetraethylene glycol · additive · 19 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 | 1069 | 0.88 | 0.90 | 150 | PG4, FAD, CL |
| 2 | 993 | 0.88 | 0.89 | 142 | PG4, FAD, CL |
| 3 | 825 | 0.87 | 0.90 | 122 | FAD, CL, PG4 |
| 4 | 469 | 0.84 | 0.91 | 72 | FAD, CL, PG4 |
| 5 | 473 | 0.84 | 0.91 | 71 | FAD, CL, PG4 |
Interfaces
12 interfaces between chains.
- C–D · 881 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 878 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 845 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 837 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 716 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4C3X · Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 · 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 Q9RA02
- Elsewhere: RCSB PDB 4C3X · PDBe 4C3X · UniProt Q9RA02
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