MolNFT v1 · #160840 · protein
E.COLI dsba in complex with benzofuran compound 26 ([6-(3- methoxyphenoxy)-1-benzofuran-3-YL]ACETIC acid)
6PVY · THIOL:DISULFIDE interchange protein dsba: “E.COLI dsba in complex with benzofuran compound 26 ([6-(3- methoxyphenoxy)-1-benzofuran-3-YL]ACETIC acid)”. X-ray diffraction, 2 ligands (OZG, CU), 4 pockets (best druggability 0.56).…
- PDB
- 6PVY
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsba
- UniProt
- P0AEG4
- Ligands
- OZG, CU
- Pockets
- 4 · best druggability 0.56
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 | 188 | 53% helix, 11% strand | P0AEG4 |
Ligands and binding sites
- OZG · [6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic acid · ligand · chains A, B
- CU · Copper (II) ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 125 | 0.56 | 0.83 | 18 | OZG |
| 2 | 237 | 0.55 | 0.77 | 32 | empty |
| 3 | 130 | 0.41 | 0.75 | 17 | empty |
| 4 | 70 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 803 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6PVY · E.coli DsbA in complex with benzofuran compound 26… · 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 0.98
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 6PVY · PDBe 6PVY · UniProt P0AEG4
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