Research workbench
Crystal structure of ecdsba in a complex with purified pyrazole 9
Analyse Crystal structure of ecdsba in a complex with purified pyrazole 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PDH
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsba
- UniProt
- P0AEG4
- Ligands
- OAV
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | THIOL:DISULFIDE interchange protein dsba | protein | 187 | 53% helix, 11% strand | P0AEG4 |
Ligands and binding sites
- OAV · 2-[4-(4-cyano-3-methylphenoxy)phenyl]-N-ethyl-N-[2-(1H-pyrazol-1-yl)ethyl]acetamide · ligand · chains A, B
- PGE · Triethylene 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 | 191 | 0.62 | 0.83 | 34 | OAV, PGE |
| 2 | 308 | 0.56 | 0.75 | 37 | empty |
| 3 | 89 | 0.39 | 0.77 | 13 | empty |
| 4 | 74 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 830 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6PDH · Crystal Structure of EcDsbA in a complex with purified pyrazole 9 · the same entry in another collection · chain A against A, TM-score 1.00
- P0AEG4 · AlphaFold monomer V2.0 prediction for THIOL:DISULFIDE interchange protein dsba (P0AEG4) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P0AEG4
- Elsewhere: RCSB PDB 6PDH · PDBe 6PDH · UniProt P0AEG4
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