Research workbench
Crystal structure of E.COLI dsba soaked with compound 4
Analyse Crystal structure of E.COLI dsba soaked with compound 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WF5
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein
- EC
- 1.8.4.2
- UniProt
- C5WBA2
- Ligands
- WF4, CU
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | THIOL:DISULFIDE interchange protein (EC 1.8.4.2) | protein | 188 | 52% helix, 11% strand | C5WBA2 |
Ligands and binding sites
- WF4 · 4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-thiazole-5-carboxylic acid · ligand · 2 copies · chains A, B
- CU · Copper (II) ion · metal · chains B
- GOL · Glycerol · additive · chains B
- EDO · 1,2-ethanediol · 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 | 225 | 0.55 | 0.77 | 37 | WF4 |
| 2 | 217 | 0.52 | 0.76 | 36 | empty |
| 3 | 107 | 0.38 | 0.75 | 17 | empty |
| 4 | 80 | 0.31 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 692 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4WF5 · Crystal structure of E.Coli DsbA soaked with compound 4 · 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 C5WBA2
- Elsewhere: RCSB PDB 4WF5 · PDBe 4WF5 · UniProt C5WBA2
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