Research workbench
Crystal structure of ecdsba in a complex with purified methylpiperazinone 6
Analyse Crystal structure of ecdsba in a complex with purified methylpiperazinone 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PC9
- Type
- protein
- Length
- 375 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsba
- UniProt
- P0AEG4
- Ligands
- O7P
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | THIOL:DISULFIDE interchange protein dsba | protein | 187 | 53% helix, 11% strand | P0AEG4 |
| B | THIOL:DISULFIDE interchange protein dsba | protein | 188 | 54% helix, 11% strand | P0AEG4 |
Ligands and binding sites
- O7P · 2-methyl-4-{4-[2-(4-methyl-3-oxopiperazin-1-yl)-2-oxoethyl]phenoxy}benzonitrile · ligand · chains A, B
- PGE · Triethylene glycol · additive · chains 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 | 139 | 0.63 | 0.86 | 23 | O7P |
| 2 | 367 | 0.60 | 0.76 | 46 | empty |
| 3 | 136 | 0.41 | 0.75 | 19 | empty |
| 4 | 100 | 0.35 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6PC9 · Crystal Structure of EcDsbA in a complex with purified methylpiperazi 6 · 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 0.97
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 6PC9 · PDBe 6PC9 · UniProt P0AEG4
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