Research workbench
Crystal structure of DPR4 IG1-IG2 in complex with dip-eta IG1-IG3
Analyse Crystal structure of DPR4 IG1-IG2 in complex with dip-eta IG1-IG3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EG0
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Defective proboscis extension response 4; Dpr-interacting protein eta, isoform B
- UniProt
- Q59DX6, Q9VMN9
- Ligands
- NAG, FUC, BMA, MAN
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Defective proboscis extension response 4 | protein | 201 | 3% helix, 51% strand | Q59DX6 |
| B | Dpr-interacting protein eta, isoform B | protein | 309 | 4% helix, 56% strand | Q9VMN9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.43 | 0.83 | 15 | ACT |
| 2 | 64 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 916 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6EG0 · Crystal structure of Dpr4 Ig1-Ig2 in complex with DIP-Eta Ig1-Ig3 · 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 Q59DX6
- Every structure of UniProt Q9VMN9
- Elsewhere: RCSB PDB 6EG0 · PDBe 6EG0 · UniProt Q59DX6 · UniProt Q9VMN9
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