Research workbench
Crystal structure of diels-alderase CE20 in complex with a product analog
Analyse Crystal structure of diels-alderase CE20 in complex with a product analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O5T
- Type
- protein
- Length
- 645 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diisopropyl-fluorophosphatase
- EC
- 3.1.8.2
- UniProt
- Q7SIG4
- Ligands
- XDA
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diisopropyl-fluorophosphatase (EC 3.1.8.2) | protein | 319 | 3% helix, 49% strand | Q7SIG4 |
| B | Diisopropyl-fluorophosphatase (EC 3.1.8.2) | protein | 326 | 5% helix, 48% strand | Q7SIG4 |
Ligands and binding sites
- XDA · 4-{[2-(phosphonooxy)ethyl]carbamoyl}benzyl [(1R,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.78 | 0.97 | 27 | empty |
| 2 | 86 | 0.76 | 0.98 | 26 | empty |
| 3 | 203 | 0.74 | 0.89 | 27 | XDA |
| 4 | 220 | 0.73 | 0.88 | 30 | XDA |
| 5 | 392 | 0.69 | 0.81 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4O5T · Crystal structure of Diels-Alderase CE20 in complex with a product analog · the same entry in another collection · chain A against A, TM-score 1.00
- Q7SIG4 · AlphaFold monomer V2.0 prediction for diisopropyl-fluorophosphatase (Q7SIG4) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q7SIG4
- Elsewhere: RCSB PDB 4O5T · PDBe 4O5T · UniProt Q7SIG4
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